I'm glad you're enjoying it!
That's very strange, though. Your custom items are saved locally and shouldn't have anything to do with Twitch connection. There's ways to make different item profiles, at the very bottom of the settings menu if I remember right. It's possible yours got corrupted somehow, or didn't save correctly. Or maybe defaulted to the wrong one for some reason?
I can't look at the folder structure right now (not at my computer) but there should be a folder within the Item Flood folder that stores all the saved data, it could be worth checking what files are in there.
In case you didn't see it, this version of Item Flood will stop working this April anyway because Twitch is depreciating the API stuff I used in it but I'm trying to have a new version released before then. So even if we can't figure out what's causing your issue, it hopefully won't happen in the new version anyway.