I'm running Pro Tools HD 2, 7.4. My MIDI I/O has been really finicky as of late and will not sync up when I open Pro Tools. I'm going to head down there soon to try and troubleshoot the damn thing but I thought I'd ask around here first to try and get some idea on where to start or if anyone has any knowledge of this happening to them. Thanks!
Never heard of this happening on an HD system. Have you tried tech support? They've gotten a lot better lately. The digi forums are a good source as well.
Cubase had a similar problem but I doubt it's the same issue. The fix was simple. Basically you needed to tell Cubase to ignore any "emulated" midi ports. This of course is likely totally unrelated.