Okay, it took me way too long to find this considering how simple it was. If you are logged in, visit:
and it will update your reputation plus give you the actual info on how it is calculated. Waaaay down at the bottom is a summary of reputation changes. This should, hopefully, fix the caching issue and trigger the correct calculation of your reputation.
There is a related question on the mother meta which seems to indicate a bug existed ~8 months ago in the update script when users hit the rep cap and then lost some votes somewhere. The answer there says the bug is/was acknowledged but I haven't found whether it has been fixed or not.
If manually updating the reputation doesn't fix it, maybe there is still a problem somewhere and this needs to be escalated.
But that's above my pay grade.
Reading into that mother meta question, particularly the comments under it, it seems that the manual refresh button was removed from that reputation page I gave and the only way to trigger a recalc (at that time) was to delete/undelete one of your own answers. Again, no idea if this bug is still around or not, but you could always give that a shot and see if things update.