Getting this same bug. PLEASE FIX adobe! Its extremly annoying!
I have no idea why someone would use FP to edit code when you get a free copy of Flash Builder with most versions of the CS Suite.
However, if for some reason you just want to do this, what happens if you "undock" the tab?
Ya, I havent used Flash Builder yet only because FP is what I'm used to. However, just imported my project into FB 4.6 and it's alot better so thanks for the tip.
So I tried undocking, and the bug remains if you copy a line from one 'undocked' tab, into a docked tab. However if both code windows are undocked, the copy/paste and window focusing works fine, but in my case with ~20 class files, it would be a nightmare.
The workaround is either edit the project in CS5.5, then open and re-save it in CS6, or in CS6 click the file tab you want to edit, then click within the file, then paste, every time you are copying a line from one file to another.