Which version of photoshop and mac os x are you using?
Are you assigning the shortcut to the Edit>Transform>Flip or Image>Image Rotation>Flip?
its CC 2014.2.2 on 10.9.5, but it happened also on 10.8 and with erlier CC versions.
i'm assigning it to Edit>Transform>Flip.
Seems to be working with photoshop cc 2014.2.2 on mac os x 10.10.1, so far.
I'd reset the photoshop preferences and see if that makes any difference.
Press and hold down the Shift+Command+Option keys just after starting the launch of photoshop
Keep holding the keys down until you get a dialog asking if you want to delete the adobe photoshop settings file
it works here too, only sometimes this shortcut gets back do the default assignment.
resetting the preferences means that i need to adjust my settings again after that?
do i loose all my presets, etc. or just the preferencies?
Mostly just the preference settings.
Any presets should still be there.