Nope, it is still happening... at least this morning, and it took me a while to get it running correctly (restarting jack would get rid of the glitches and a short while later they would be back - ended up rebooting the card just in case). I have it working without problems again, and it has been fine for the afternoon. I don't know why sometimes I get into this glitchy mode.
I was trying to learn a little bit more about the quirks and found what may be an unexplained "bit" in the Motu quirk table I have...
For this endpoint in interface 5:
.ifnum = 5,
.ep_attr = 37,
Binary: 37 -> 100101
(there are three two bit fields in this 6 bit number)
0x03: XFERTYPE_MASK -> 01 -> USB_ENDPOINT_XFER_ISOC
0x0c: USB_ENDPOINT_SYNCTYPE -> 01 -> USB_ENDPOINT_SYNC_ASYNC
0x30: USB_ENDPOINT_INTRTYPE -> 10 -> ?
It seems to me this last two bit field (interrupt type) should be either 00 or 01, 10 is not decoded anywhere that I can see in the software (and would be treated in xhci.c as 00). I imagine the intention might have been to set this to 01 (which is USB_ENDPOINT_INTR_NOTIFICATION).
But looking at the code in xhci.c it seems to be this would be unused anyway, this two bit field is only "decoded" if the endpoint is USB_ENDPOINT_XFER_INT, and we already defined it as USB_ENDPOINT_XFER_ISOC. So there is an extra bit? (which does not hurt - I though I had found a bug but it does not seem to be the case).
I went ahead and replaced "37" by "21" (010101), just to see what happened, built modules, installed and restarted the driver. It still works as before and there are no glitches so far. But I am sure there will be some I'll report back...