On Windows XP Pro SP2.
If the uninstaller is executed by standard users, the installer can't detect POPFile is running.
Here's the part of the uninstall log:
POPFile 'ServiceCall?' response: openerr
Checking 'C:\Program Files\POPFile\popfileb.exe' ...
Checking 'C:\Program Files\POPFile\popfileib.exe' ...
Checking 'C:\Program Files\POPFile\popfilef.exe' ...
Checking 'C:\Program Files\POPFile\popfileif.exe' ...
Checking 'C:\Program Files\POPFile\wperl.exe' ...
Checking 'C:\Program Files\POPFile\perl.exe' ...
Checking 'C:\Program Files\POPFile\pfimsgcapture.exe' ...
Checking 'C:\Program Files\POPFile\msgcapture.exe' ...
Checking 'C:\Program Files\POPFile\stop_pf.exe' ...
Checking 'C:\Program Files\POPFile\pfidiag.exe' ...
<snip>
So the uninstaller can't delete locked files. (e.g. POPFile executable, DLLs)