I can imagine three things.
1) Either it's a real bug. But there hasn't been any change in the code related to this for months, so not likely.
2) The reviewers in the country has made a huge cleanup and archived a lot. This takes time for Project-GC to detect. The syndrome is explained in the FAQ (http://project-gc.com/Home/FAQ#04b709aeade6ef3032cf4d3a1e2b9dd0) under "My found count isn't correct".
This can be due to many reasons. If you have deleted logs, Project-GC might not have detected it yet. The logs you have created the last two days might not be detected yet either. But this should normally not be a consistent issue. Project-GC is trying its best to sync up every profile, and users of Project-GC gets a higher priority and normally gets a sync about daily. But there is at least one case that can not be solved via the Geocaching LIVE API. Geocaching.com is showing finds a bit inconsistently sometimes. If your profile on Geocaching.com lists 100 finds but you only see 99 when you list all your finds there, then Project-GC will just show the 99. The reason behind this is that one of your logged caches has been retracted. It has been removed after being published. Not just archived, but a reviewer has been taking the cache back for some reason. These can not be seen by Project-GC, this is a design from Groundspeak and not something we can do anything about as it works today. As mentioned, these aren't listed anywhere on Geocaching.com either.
Added to this, there is also the Lab caches, which aren't supposed to show up in statistics. They do not exist in the API and Project-GC does not handle them at all.
3) You accidently read on the wrong side. One of the sides splits on 500 (actually a bit below) and the other side on 1000 (990).
It would help a lot if you could tell us which filters you used, or add a link after applying the filters.