Check your routing thoroughly.
How are you monitoring? Via hardware, or via the cue sends in the tracks?
Sounds like a phasing issue. Does the main mix sound empty in the middle or diffused compared to the cue mix?
If so, then a phase switch in one channel, after the cue mix point, is on. You could have accidently flipped it on in the Pre rack (p194 in the Op Manual) and hidden it, or in the Control Room.