If a custom item is generated, it doesn't show up in the Purchase screen to be bought. However, I can create and buy one if I click on "Buy" instead of "OK" when in the "Customizing Item" screen. It makes it over to the inventory screen in that case, but I have to customize a new one every time if I want to have more than one of a particular customized item.
A couple of examples (try customizing these to duplicate):
Banded Mail +1
So far I've managed to have this happen with weapons, armor, and wondrous items (headbands), 3/3 of the item types I've tested so far. I've testing it in both 3.5 and PF, so this problem doesn't seem peculiar to one game mode.
Wanted to chime in and say this is happening for me as well. Using PCGen v6.04.01 with Java 1.7 on my desktop and 1.8 on my laptop and both experience the issue. Any custom item I try to create does not appear in the purchase list if I click OK, I have to click Buy to have it appear in the character's equipment and recreate it every time.
I don't work with Java so I am not sure how to fix it but I think I traced the issue to line 3595 in gui2/facade/CharacterFacadeImpl.java. The if condition seems to fail on "dataSet.getEquipment() instanceof DefaultListFacade<?>" and so it skips trying to add a new element to the equipment dataset.
My lack of knowledge with Java and the codebase stopped me from knowing what to do to either convert the returned equipment object into that type of set or if it was replaced with a new set type and needs the methods and condition to be adjusted from a previous update. Just hope this can help someone more familiar with Java pinpoint the issue and get a fix in.
Thanks for tracing it back to that line - it made the fix much quicker.