I decided to add another one that has been driving me crazy lately, although it is arguable that it may actualy be "working as intended".
That is every time I log my fighter or barbarian, power attack is turned off. I have heard this affects some rogue abilities as well, but I don't have any details about those. Since almost all abilities, now including metamagic feats, remain in the state the user left them in, while power attack and a handful of others always get shut off I don't think this is working as intended, and is at least inconsistent, confusing and annoying for the very few abilities that you have to remember to turn on every time you log.
I added it above - I consider it a well known issue, and not working as intended since having some abilities automatically turn off while most do not is inconsistent and seems like something that should be fixed.
Thanks
Issip