I hope I describe my problem well enough.
Up until today, with my settings, my Mini-List would just show me Things that I can actually collect with my current character (usually Mail-armor etc with my hunter). At the same time, I use the tooltip on (mostly green) BoE items in my bag to see if I have collected them and send them to alts if I don't have them yet (cloth to my priest etc).
Somehow, starting today, the Mini-List and Bag-Tooltip are somehow synced with each other, meaning now I only get the "Collected" / "not collected" in the topright corner of my bag-tooltip on items, my hunter can actually use. If I turn on Account Mode, I see the tooltip properly again, but now my Mini-List is also full of cloth, leather and plate stuff, which I do not like.

What changed and how can I adjust my settings that it works as before?

This is already fixed in the development version and will be in the next release. You can install latest alpha version through your addon manager or directly from here, it is fixed there.