Our suspicion is that your problem is caused by some interaction between your rather sophisticated setup and some possible incipient weakness in the H9. As mentioned above, you should certainly consider sending your unit in to be checked, but it is likely that without access to your other equipment we will find nothing wrong with it.
My guess is that you are unknowingly sending it a lot more than just MIDI clock, and that this is overflowing the H9's internal storage while the unit is otherwise occupied loading a preset. I'm inclined not to believe that just MIDIclock would do this, unless you are running at 1000 BPM.
Because the H9 is, at the end of the day, just a guitar pedal, there is a limit to the amount of MIDI it can handle. Obviously we intend to increase this as much as possible, but …
I would suggest three options:
1) Send the unit in for us to have a look (see above comments)
2) Find another way to generate a more limited MIDIclock.
3) Return the unit to your dealer.