Stephen,

It's a known issue over on the TDIClub (http://tdiclub.com) for all of the
common-rail TDIs. You may have gotten a newer revision fuel pump with the
replacement. You can count yourself lucky that the stealership warrantied
the work and parts. Some reported having to pay out of pocket.
Another known issue is icing in the intercooler line.

I have not experienced either issue with my '11 Golf, but I drive the car
like I stole it, and change both the fuel and oil filters at the 10kmile
interval rather than waiting 20kmiles for the fuel filter.

It is a Volkswagen after all.

Cheers,
Sudhir