Jim,
Sony and Pro Tools issues are different. With Sony's Vega NLE for video, the best way to make it happy is to temporarily uninstall MC, install Vega, reinstall MC. Then everything seems to be fine. That was as of version 12 of Vega, which is the newest I've had installed here.
The PT issue described by the OP is not the same, and as I stated above, is probably being caused by trying to use non-Digi/Avid compatible drivers, not MC. I checked my MC ASIO configuration and found that it has not been disabled, yet PT works fine with its Profire ASIO driver. Later versions than mine also will. I have had version 9 and 10 installed and working here. MC is always running and causes no problems.
--Bill