C:\Program Files\Digidesign\Drivers\MMERefresh.exe
Boot your computer, but don't boot pro tools. Go to the drive you have pro tools on and go to Program Files-->Digidesign-->Drivers-->MMERefresh.exe
Double click MMERefresh, and restart the computer. Boot pro tools, go inside the midi beat clock settings and check the appropriate midi boxes (digi 002, or whatever device it is you want to use midi for.)
Let me know if this works.