Very strange. I use FMPA 13 on 10.7.5 and have never seen this. I suspect this is an OS X issue rather than a FileMaker issue. Does this happen with any other applications?
Only FMPAdv 11 (as far as I remember). It's a few weeks or months between occurrences, so I haven't given it a lot of thought, just re-launch & keep moving. But today I decided to post about it.
I also experience this… sometimes.
In my case, activate Finder on the Dock and then, activate FileMaker Pro on the Dock fixed the issue. No need to quit.
I can also use the cmd-tab combination instead of Dock to switch apps.
And true, i also think i didn't experienced this with very recent version of FileMaker.