I entered ICC today to farm old content, and had my raid difficulty set to “heroic” before I entered. I went and killed a couple of bosses… only to then notice that the difficulty was on “normal” somehow. With the 9.0 patch you are no longer able to change the difficulty inside ICC between normal and heroic. I exited the instance and had to switch between raid difficulties several times before the skull finally appeared in the raid portal door… but then I could not enter, because “You are ineligible to participate in at least one encounter in this instance because you are already locked to an instance in which it has been defeated.” I expect that the old “switch difficulty on the fly” structure for ICC could be causing problems with how it recognizes our raid settings before we enter.
I have the same issue. Confirmed that my legacy raid preferences were set to 25 man Heroic but it was 25 normal. Once I killed the first boss I was locked to 25 normal with the new change and couldn’t do heroic.
They need to fix the difficulty changing. It breaks lockout sharing and is super annoying for problems like you state as well.
This happens with Ulduar and Naxx , so seems lich raids are for sure doing it
Same exact thing happened to me. Killed many bosses to then realize I was in normal ! Even though the difficulty was set to Heroic !!!
Same thing happened to me with icc. Using saved instance tracker, I can see my first two toons did indeed complete heroic. However, I did two more, and it was only after getting un collected loot on the last one I realized something was up. Even after doing heroic cata raids, and my instance panel being set to heroic 25, I was locked to a normal 25. Not the biggest deal, but definitely mildly enraging
This is still happening. I noticed that if I’m outside of the entrance and drop it down to Normal and then back to Heroic, it will work. But if it’s set to Heroic from farming other raids and I just go in, it will set it to Normal despite displaying under my Instance Options setting as Heroic.
This is still happening, come on Blizz…fix this issue
Still happening. Makes it really annoying when trying to farm for Invincible. 
This is still happening! There’s no excuse for Blizzard. They make enough money they can hire people to fix this.