I don't have
aot=1, so I added that to my reaper.ini and it acts like you describe! So try changing that to =0 or just remove that line.
Hmmm, AOT is usually short for Always On Top, but I don't see an option in REAPER for that.
EDIT: Main Menu > View > Always On Top
I didn't see that option because its hidden in my custom menu, but enabling that adds
aot=1 to the ini file.