I had a very similar experience to Brad Feld this summer. I had swapped cars with my brother and gone to the DMV to fill out the paperwork and paid all the fees so everything was legal.
I got pulled over a year later and was told that my license plate didn't match the car it was registered to (similar situation to what you experienced). Luckily the officer understood that this was a DMV error and told me to clear it up with them.
The most frustrating part was then going to the DMV and having them accuse me of losing the paperwork and to "check with my wife" who was probably more responsible than I was. 2 days later the DMV sends me the paperwork that THEY had neglected to mail me earlier and wanted me to fill out.
$600 dollars worth of fines and 2 days of my life that I'll never get back but we finally got it resolved.