well... if you dont get clipping on tracking, the problem is narrowed down.
if i understand correctly, your unprocessed, master channel is clipping? Is this because the dynamic are reaching more then "0" db? just so you know, that is the max threshold, set by the software your using so you have unity in your recordings. anything going about this threshold is going to be limited or distorted, which is completely undesired because the master track isnt a plugin, nor is it meant to be clipped. so to start, set all your tracks to a volume so that NOTHING surpasses "0" db on the master track.
also if you know this and do this... this could be you dsp maxing out. Does clipping happen when you have a lot of plugins in?
and lastly, the only other thing i can think of is that you have a really slow release time on these instruments and a mid to slow attack time with HUGE amounts of GR going on. what happens if your track is too compressed and set with a long release time is theres no volume going back to unity gain, and its a sure sign of too much compression for drums, vocals and overheads IF your pushing constantly more then 8db of GR. If the meter never goes back to 2db to 0db of GR, than this might suggest you get loud transients popping through which might make you master channel clip, especially if your turning gain compensation way up. so if this is the case, find a section where the instrument pauses for lets say, 4 seconds and starts again loud after that. if theres a a loud clip there, this could be your problem. if it is, use way faster release times, and less threshold, different ratios. maybe find a tutorial or something on here about compression.
hope my suggestions help, dont mean to insult you if you do know these things, just wanted to help.
