I assume the ROMS you mean are Pokemon Gold/silver/crystal. I don't think you can sync time in-game (cause what if you did the Rockbox save thing before a hard fight? also, that would mean that Rockboy would tecchnically be running all the time to keep up with the real time)
I also used a GBC emulator, and this is what happened, so my guess is based on that, and playing the Game on my Ipod video.
Without pratically re-writing the code for rockboy, I don't think this can Happen.