I have trouble with the quota too. I get a report from one user who cant recive any pm's. The system told the sender that the reciver ist over the limit of 200. I check the reciver and he have 3 messages. I delete all 3 messages so he have 0 but the problem still exists. I run the maintenance scripts for pm's but this dont help.
I raise the the limit for all user from 200 to 250 and the user can now receiv messages again.