This is an issue I have dealt with the entire time while using CS6. Adobe indicated to me they were working on the problem so I just KNEW it would be fixed for CC. But, apparently not. Excerpts from my previous post:
I work in separate windows when using Ai and Ps (not tabs). Machine is a Mac running Mountain Lion. I minimize windows frequently and click back into them when needed. When I'm working in another app, and then click a minimized Ai or Ps window, the desired window pops up but another window (from the same app) jumps up in front of it. An additional example: if I close an Ai file and happen to have a minimized Ai window in the dock, when the active file closes, the minimized window pops up. It is annoying & disruptive. Neither Application Frame nor OS Mission Control settings have had any bearing on this issue. CS5 did not do this. It started with CS6 and now, unfortunately, continues with CC. I believe this is a universal issue as Adobe was able to replicate and we were able to replicate as well on other machines. Anyone else dealing with this or is everyone working in tabs?
Dear Adobe - any updates??