Hi CheepinC_altera,
Thanks for your note! I have indeed looked into this already.
As far as I can tell, I think it must be an issue with the reset sequence, as the data does seem to loopback correctly every so often. This may indicate an issue with the CDR lock, right? Especially as signal taps reports that the on the TX parallel bus is as expected each time.
I am hoping someone might notice what I have done differently enough from the reference designs to cause this intermittent issue.
I have combed through both my design above and the reference design a few times and seem to keep missing whatever the key difference is.
Many thanks