Hi Mark,
Did you have the Index input floating?
If so it might pick up noise from the adjacent lines causing the counter to roll over. Anyway, that's not the way you're supposed to have it configured for what you're doing - as you've discovered.
Any chanse you were looking at the first four digits of the POSCNT register(s) and missed the fact that it DID roll over to 65535?
2767 -> (6)5535 -> 0 or 2767 -> 0 -> (6)5535
Anyway, I'm glad you're back up and running.
/Henrik.
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