I think it feels particularly bad because when I started writing the pirate AU, I was two thirds of the way through a story that was just not inspiring me*. I procrastinated like mad before writing, every scene was painful, and I'd managed about 35 pages in three weeks. I then leapt gleefully into the pirate story** and wrote 96 pages in a week and adored every minute. The contrast was very striking. But also refreshing, since the problems I was having with the other story were causing me to do my usual "Oh no! I've forgotten how to write! I'll never write a good story again!" anxiety.
* Note to self: Do not try to write a story in which every single one of your characters: A, have no idea who they are; B, as well as that, are acting increasingly out of character for external reasons: C, (as a result of A), can't be referred to by name, so you have a sea of "hes" and "hims."
** Unusual for me, since I'm strictly monogamous on my writing, and only ever have one multi-part story on the go at a time. When I see people who are juggling multiple AUs, I'm in awe. My brain just doesn't work that way.