The developers maintain that the SCIU's merchant inventory refreshes normally. This is only partially true. Yes, the SCIU will restock items it normally carries. What it won't do, is remove any items you've sold to it, even though it should. This can be easily tested by selling it something it wouldn't otherwise stock itself, like a Jar of Cloud Residue. If you sell it this or any other item, that item will always remain in it's stock. Always. It will never be removed unless you buy it back yourself. This is not true in the case of vendors like Miguel and other vendors around the Mojave who will completely refresh their inventory (replenishing their usual stock and removing items it purchased from the player).
Furthermore, besides retaining every item sold to it by the player, the SCIU will also retain every cap it makes from you. Once it's balance gets up to the 61k - 66k mark (I couldn't get a precise figure in my testing), another problem arises in that the SCIU's balance will never reduce below that point. No matter how much you sell to it. Some of you are probably finding that your SCIU's caps balance won't reduce below 65k. This leads to inadvertent "rip-offs." For example, if your SCIU has 70k caps, and you attempt to sell it 30k worth of equipment, you're only going to get around 5k caps for the sale, even though the trade window indicates you should be getting much more.
The only way to avoid this is to keep it's balance below that 60kish area. But since the SCIU won't reduce it's own caps balance to it's standard minimum (which seems to be 14k, although this could be dependent on the player's level), then this can only be done by:
1) Selling items back to it. So, if you're regularly using it for 100% repairs, or buying things from it like powder/primer packs on a regular basis, you'd need to offset these purchase by selling things to it so that it's balance never gets too high. Bear in mind though that if you do this, whatever you sell it will remain in it's inventory. Eventually this could lead to the SCIU becoming like an overfilled storage container where you experience a bit of lag before being able to view it's contents.
2) Just not dealing with the damned thing. This is the option I'm exercising until they finally fix it. I'd rather live without the new weapon mods for the meantime, and do my 100% repairs and sales transactions through other NPCs, than have them patch the thing and finding out afterwards that the patch doesn't work retroactively.
Alright, now onto the SCIU vendor testing comparisons with Miguel and Contreras...
Miguel
Miguel is an example of a vendor who doesn't seem to have any obvious problems. He regularly refreshes his inventory whether or not you're in his cell (some vendors like Blake and the Grub N Glub vendors won't refresh unless you wait for 3 days in their location or if you just happen to be in their cell at the time they're supposed to refresh). If you sell an item to Miguel, it will be removed from his inventory upon refresh. If you buy items from Miguel, thereby increasing his caps balance, his balance will reduce back to what it's normally meant to be upon refresh. Miguel is a reliable vendor with no bugs associated with him (at least none that have been reported on the wiki) and therefore served as my control in this experiment.
Okay, so play along at home, if you'd like. Enter the Pawn Shop. Before dealing with Miguel, go into pickpocket mode and check to see what he's carrying (there's a reason for this which will become apparent when we get to Daniel Contreras). In my case, he was carrying a 9mm round, some 9mm casings, and a Stimpak. First, sell him something. It doesn't matter what. After selling him something, exit dialogue and go back into pickpocket mode. There shouldn't be any change. Now start buying things from him. It doesn't matter what or how much, just make sure that when you're done buying from him, he's got more caps in his inventory than he did when you first entered. Now exit dialogue, go back into pickpocket mode and check him out again. There still shouldn't be any change from the time you first pickpocket-checked him. His personal inventory and merchant inventory are completely unrelated, and this is how it should be with all vendors.
Daniel Contreras
Contreras is a mess. Like the SCIU, he'll regularly restock the things he's meant to carry (most notably Ultrajet, which is probably what many of you use him for if you deal with him at all) , but again, like the SCIU any items sold to Contreras will remain in his inventory permanently, and he won't reduce his caps balance to normal (8k at higher levels) upon refresh.
Okay, so again, playing along at home, approach Contreras in pickpocket mode. What you see in his pocket is going to be dependent on how extensively you've dealt with him before. If you've at any point sold him armor or clothing with any DT rating whatsoever, he'll be wearing that piece of armor/clothing and his default Roving Trader Outfit will be found in his pocket. If you've sold him a number of armors, he'll be wearing the one with the highest DT rating and the rest will be found in his pocket. In fact, anything Contreras has acquired from you (caps, items) can all be his pocket. In trade mode, take note of his caps balance. Buy something from him and take note of how much the purchase was. Now go into pickpocket mode and check him out. The caps in his pocket should have increased by that amount (i.e. if he had 1k caps in his pocket, and you make a 3k purchase from him, he should now have 4k in his pocket).
Anyway, regardless of what dealings you've previously had with Contreras, do the following: Buy all the Ultrajet he has for sale. Now sell him something (not armor because he may equip it depending on it's DT rating). For example, sell him Formal Wear (no DT and hence he won't equip it). Now go outside and wait for 3 days.
When you come back, he should have Ultrajet available again. So, he's refreshed his inventory as he's meant to, but he hasn't flushed it of any previous transactions with you. The Formal Wear will still be there, and his caps balance won't have reduced (assuming it was already over 8k when you left the building). But the Formal Wear can be found in his pocket, and so can any amount of caps he might have there. It all goes into his pocket. Everything. Every cap, and every item. Now, if you allow his caps balance to reach that 61k to 66k area, you're going to encounter the exact same issue with him that you might be encountering with your SCIU in that this balance won't ever reduce below that figure.
Another odd thing about Contreras is that there's a number of containers in his supply shack. Some of these might hold some things like ammo and caps (as it did in my case). These seem to be tied into his merchant inventory. If you steal the caps in these containers, his balance will reduce by that amount. If you see any items in these containers, he should have the same items on sale. If you steal these items, he won't have them on sale anymore. Even weirder, if you put something IN these containers, Contreras will immediately make that item available for sale, even though it's technically yours. I put one of those Atomic Valence headwear thingies into a filing cabinet upstairs, went back downstairs, opened trade with him, and he had it up for sale. The bastard.
It's my understanding that once Contreras is imprisoned, the above is no longer an issue, but I've yet to confirm this. I sided with Contreras in my game, so I can't tell. Perhaps someone else might know.
SCIU
See above. Everything that applies to Contreras applies here. The SCIU will restock, but it won't remove items sold to it by the player and it will retain all caps acquired by the player. Unlike Contreras, the SCIU is not a proper NPC. It's an object, and therefore can't be pickpocketed. If you've used your SCIU extensively for vending, chances are, it either has an abnormally high balance that can't ever be brought back down to zero no matter what you do (and might rip you off) or it's still holding every item you've ever sold it. Or both.
In any event, this is not how vendors should be functioning. They should all be functioning as Miguel does. I'm aware that numerous people were involved in the development of this game, but is it so difficult to ensure that, when it comes to programming vendors, that everyone is on the same page and programming them the same way? Granted the SCIU is a new object, but Contreras has been bugged in the manner described since DAY ONE. Surely, I'm not the first player to report this. As I play on XBox, I don't even have a GECK and it's much more difficult for me to figure things out without one.
(Big thanks to vometia for confirming on her GECK that Contreras and the SCIU were set up similarly)