(I have posted this issue before and never solved this - is no one else seeing this?)
I have removed FW prefs and un/reinstalled CS4Pro (Mac), threw out all Adobe prefs and still I am getting incredibly bizzare Applications Bar issues. Everytime I open a file, the Title Bar of the file is pushed up behind the Applications Bar - to the top-left of the available screen. I have to cycle Windows > Use Application Frame off and on, until the window(s) come back in cascading view. The Application Frame tabs only works if I have one file open - if I open a second file, I get a completely impossible window with the Title Bar tucked under the Mac's Menu Bar (see attached image). Cycling through Use Application Frame gets the Title Bar back. Weird, right?
Have you tried posting your question in the Apple forums? [discussions.apple.com] They are generally very good at tracking down problems like this.