I am attempting to add some weapons to a merchant chest using leveled lists, so appropriate leveled items appear based on the player's level. I have tried various methods of this; items in a leveled list that goes in the container, items in their own leveled list which each go in another leveled list that then goes in the container, etc., however for some reason no matter what I try, including entering ridiculous count numbers and zero chance for zero, calculate from all levels <= pc's level and calculate for each item in count, the game will frequently not include various item's appropriate to my level in the list.

In my experience "calculate for each item in count" appears to do nothing. In other words, say I have two items in my leveled list, both set at level 18. If I enter level 18 as the preview level and set preview count to two, I randomly end up quite often with two of only one of the items, no matter whether this box is checked or not.

I see other mods have had issues with this and haven't been able to find any specific documentation this far. Any suggestions?

There's an issue with the random number generator that makes it come up with the same answer several times in a row when it's called repeatedly in quick succession, so it can easily behave that way. I don't recall if that's a CS problem, or if it happens in-game too. If you want a good mixture of items (and levels) check the "calculate for each item" option as well as the "<= PC level" one, and remember to do it at each level if you nest lists.