I've made it to the point in the game where I have a bunch of crap, and too few store to sell them, so I decided to make ALL the stores in the starting town. I also made a few stores in the adjacent town.

In the first town, I sell so much crap that I use up ALL the money in all the stores. When I go to my second town, those stores also have no money left.

Very minor spoiler with names, if the above was not clear:

I build the level 3 (max) version of the Weapon store in Sanctuary and in Abernathy Farm. Let's pretend the Weapon Store starts with 515 worth of caps in cash. When I sell 513 worth of caps to him in Sanctuary, he will be left with 2 caps. Then I travel to Abernathy Farm and visit the Weapon Store there. That store also has only 2 caps left!

Can anyone else confirm this?

Are the two towns ties together by Supply Chains? Maybe that somehow links the vendors? Seems odd, I'll say that. If a vendor in Sanctuary runs out of money I fail to see how that would affect a vendor in Abernathy Farms. I know you can wait a few days and their currency resets (there is a mod that reduces the time for vendor-fund to recharge)....

I'm not that far along in the settlement building to confirm but that sounds like a bug to me. Perhaps others can confirm?

Yes, having the same issue. Not sure if it is even an "issue," per se. I'll probably run some tests later tonight (unless someone can answer it now) and see if linking settlements has anything to do with it.

There's still the added benefit of having a passive income from stores in each settlement, though. Going town to town and collecting 2,000+ caps from each after several days is pretty nice.

Hmm, I mega built shopping mall in samctuary so i dont need to go elsewhere to sell, but I do have shops in other settlements for banking the caps they generate.

Let me check and see if I have this issue of OP and will edit post.

This happens to me too with linked settlements - not sure if it happens with solo settlements too - will have to test it

I've tried a few simple tests and stopped as I don't seem to have the issue - my stores work as it seems intended, separate caps inventory.

1- bought stuff at Tier2 trading store in Sanctuary to reduce caps supply, went to Abernathy farm - same tier2 trading store has different cap supply (as expected)

2- tried above via both run to Abernathy and via fast travel, no difference

Seems like OP has bugged save game. Maybe storing all your stores, then re-setting them up will reboot them?

Are they both linked to each other? I.e. have a trade caravan running between them.

Hmm. Thanks for checking. It seems more than a few have the same problem as me.

My settlements are all connected.

They were, I have reverse routes running from most my settlements to Sanctuary (to save on population hit as I use Sanctuary as largest pop to boost store income).

In the test I did, I had route going from Abernathy to Sanctuary, and my store incomes for identical tier trade stores present at both locations were different. I also have a tier3 trade emporium, but I only have one of that and could not test that tier.

Given that we know there is at least 1 bug that is specific to store tier - the weapon tier 1 shop which has a problem for many people being able to assign settlers or keep them assigned to it, while tier 2/3 work just fine, maybe OP should post what exact store type and tier it was.