This answer is in addition to Jon's comment, which I'm fairly certain is one reason for this to happen.
When I only had 5 spam flags I had this happen to me quite a few times, where I'd flag 5 answers as spam and a moderator would go in and delete them, and I'd get my 5 flags back. This might be dependant on exactly how the flag is handled and also what kind of flag it is, and I'm not sure if it happens anymore since it's not as easy keeping track of the number of flags left now.
Though I think there's the same or at least a similar issue with flag weight. A few days ago I flagged a bunch of answers as spam, and later I noticed that my flag weight had gone up, but a little later I noticed that my flag weight had gone down to the exact number as it was previous to flagging those answers. All the answers were from the same user, so I assumed that maybe a mod had deleted the whole user account and all related posts and this might be side effect.