Yeah, I've done quiet a few tests since I started the thread including some blind tests and I can't hear the difference now.
It is possible that the signal was being doubled up when I first noticed a problem a few months back as I haven't entirely got my head around the routing in Apogees Maestro application which I find unnecessarily complicated, but I think I would have noticed if it had been comb filtering.
I used to use plug ins so maybe some artifacts were being introduced at difference buffer sizes, I wouldn't really know, but I tend not to use them these days preferring the analogue gear. Maybe that's why I can't hear a difference now. Looks like I need to do a few more tests.