Protools 9/10 is very finnicky about how it interfaces with ASIO/ DM desks. If one setting is wrong, the session freezes temporarlily and you'll get nasty contentions such as "You're running out of memory!" Or: 'Elastic Audio can't keep up! Set Elastic Audio to Render Mode, or disable some native plug ins!" In fact, neither of those things is necessarily true, nor will addressing them affect anything. The issue lies elsewhere, and it's likely either in a USB link or in MTC/MMC/HUI.
USB hubs can cause all manner of disconnects; if you've been in an automated mix session, pushed a DM fader and suddenly had the session freeze while one of those annoying warnings pops up - it's likely because of a USB messup. The solution is to either remove the hub, or unplug all inputs and let your PC do the plug-play routine again. Occasionally, a cold boot of your PC does the trick.
Check your USB portals too; could be a conflict there. In my experience, it's not necessary to dedicate a MIDI cable to MTC; USB should be stable assuming there are no conflict issues. Finally, make sure your DM Midi settings are 'plumbed' the right way; this can get a little confusing, but if you want, I can try to upload a screenshot of how I have my DM set.
With PT, you need two separate HUI/Mackie settings in the DM: one for tracking, editing, and arranging; another for automated mixing The former configuration makes PT the timecode master; the latter is the reverse. Why is this necessary? Because you'll lose the RECord transport button from the DM's control surface if you allow PT to generate timecode. You don't need that capability in auto-mixing, so it's not an issue.
For tracking/editing, use the 'Mackie Emulate' option with USB 5/6. Set the PT transport to GENerate timecode (the blue button to the right), and be sure MTC/USB3 is chosen in the Peripherals menu. When using the DM for automated mixing, you'll need to choose 'Generate Internal' timecode on the DM and tick the EXTernal timecode option in the Automation Menu. In the HUI menu, enable the Generate Internal Transport 'button.' Then, in the PT menu, DISABLE generate timecode on the transport, Enable MMC in the Peripherals menu, and put the PT transport into ONLINE (the two blue buttons which flash).
Once all of this is set up, the configurations can be saved to a template or snapshot - making the switchover easy and painless.
I hope some of this helps, and you get your timecode issues ironed out.
CaptDan