Yes, there is a Perl executable called Wperl just for this purpose. Create a batch file in notepad with the following contents and save it as STARTPF.BAT

C:\
CD C:\POPFILE\
WPERL.EXE POPFILE.PL 
EXIT

Modify the path for your particular configuration. Running this command will start POPFile in the background.

Note: Running Perl in the background using Wperl will hide any errors that would normally display in the DOS box when you are having problems.