There's a thread in xda about this. I had/have the same issue, my workaround is after the phone call is connected, I hit the home button, then turn off the screen. The flashing on/off thing seems to be limited to the call in progress screen while on bluetooth. If you go off that screen, the timeout and screen button both work and the screen stays off. So many calls went to mute or hung up since phone was in pocket while using bluetooth, now no worries, just gotta remember to hit home, then power off screen.