Hi.
I'm not sure I can help but how are you getting the audio out from the DAW to the storage device? Is the drive the same as the root drive? Does the drive meet specifications with the DAW? It has been suggested that the drive the program is on and the destination drive be different, and 7200 rpm's is suggested. I have had success with lower track count (and lower processing demand) on lower RPM drives but the casualty might be quality...It kind of sounds like you have phase issues somewhere...If your using an external drive to record/mixdown to have you tried a different cable? Be it firewire, USB, and have you tried shorter higher quality cables? Final thought, make sure all your drivers are up to date for your system and maybe even re-install Studio one/3 and see what happens. Short of that the only thing I could suggest is try defeating all the processing and see if it still exhibits the same issues. If this helps then run through the plugins and see what causes problems.
Best regards