Couple of thoughts. I've been using Flexi 12 for a bit now...
Check your soft proof function if it's on or off. That makes a difference on how things appear on your screen.
Also, Flexi doesn't like to play well with photos that are set to CMYK. Every time I drag a photo into Flexi that is CMYK and not RGB, it is completely blown out on color. Try converting it into RGB in Photoshop and replace it to see what happens.