I've run into a similar situation in the past when setting these programs to auto run on startup. It's not so much an issue with MPC Tools as it is Windows. When setting a program up to autorun, you can't easily tell windows when to load the program in it's startup cycle. As a result, it seems Windows can sometimes start a program before the necessary dependency is running. You'll find that sometimes the program loads properly, and other times it won't.
My solution to this problem on a few fixed installs is to run a *.bat script that will call on the loading of MPC. Drag the script into the Startup folder and it will execute when windows runs. Here is the file I use. This will bring up a command prompt with a countdown timer that will execute the loading of MPC.
timeout /t 20 /nobreak
start "" "C:\Program Files (x86)\Martin Professional\Maxxyz\Binaries\Maxxyz.exe"