I've setup a few filters to prevent ClamWin from scanning certain directories, but those directories still show up in the virus reports from the scheduled scans.

There are 2 different filters. One is "Exclude Matching Filenames" and the other is "Scan Only Matching File names". Did you make sure you put it in the correct one? I believe also when you set up a scheduled scan, you can set it to scan only certain directories. Some directories you might want to scan is system32, sysWOW64 (if you have a 64 bit system), appdata, memory, and registry.

When you whitelist entire folders, you have to get it just right for ClamWin. Try something like this: C:\programs\clamwin\bin\*

This makes sure that you will exclude everything in the folder. Remember that if you scan an individual file in that folder, ClamWin will still scan it.

Regards,