Earlier today, my reputation total was 3,021 (as my meta user now shows). However, the main site now lists it as 2,546. I've heard something about reputation recalculation causing small variances in rep. totals, but this is a major difference. What could cause this to happen?
There's a script that looks for "suspicious" voting patterns between users. The details are kept intentionally vague, and normally you shouldn't ever be aware of it.
Normally reputation does fluctuate by much smaller amounts, but in this case it looks like someone just got too enthusiastic and upvoted enough of your posts to make the script think something untoward was going on.