I haven't afforded the dedicated flash yet, so I still use the built in flash when I need it. Check through your entire EXIF information on one of the bad photos to make sure the EV wasn't changed somehow or that the flash balance wasn't changed either. Sounds dumb, but I have had problems bumping the main dial without knowing it; I now know that I should use the lock button on it so I don't wind up with more EV -1.5 and -2.0 pictures. Hopefully you're more careful of those settings though. Asides from that, I can only suggest double checking the color profile of your monitor and the working space of photoshop.