Hi Dietz, thanks for responding.
MIR is using ADAT3+4 for output, which is routed through the RayDAT internal mixer to ADAT3+4 input.
Cubase has ADAT3+4 input as the "input" in VST connections, and ADAT1+2 as output. The buffer on the RME is 256. The multiplier on MIR right now is x16. (i kept increasing it because I also suspected that the pops were due to not having enough latency for MIR to handle all the instruments).
Also, before the RayDAT I had 2 M-Audio cards and I made MIR use one and Cubase the other. The output from MIR into Cubase was using spdif cable. I had the exact same problem, this is the main reason I bought an RME just to be sure :(
It might be worth noting that there is a guaranteed pop and/or total silence for half a second when I maximize or minimize a process with a priority set to "high" like Cubase... is this due to me having lowered the MIR process to "normal"?