What's wrong is that there is no error message or output. Unless there was one and you forgot to tell us ;-).

On Windows strings are delimited by " rather than '. It does output an error when I try this: echo '^(GUI_|AA_|myMainScript)'
'AA_' is not recognized as an internal or external command, operable program or batch file.

Sorry for forgetting the error message. Both using ' and " does output an error saying that the command myMainScript (in the regex) is written wrongly. On a Unix system the same works perfectly, but I am not quite sure how to write my Regex in the command line on a Windows machine...

On a Unix system the same works perfectly, but I am not quite sure how to write my Regex in the command line on a Windows machine...

Avoid the commandline, write a program.

#!/usr/bin/perl --
use strict;
use warnings;
system 'pp.bat', ...;
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pp.bat ain't nothing but use pp; pp->go;

This reply is rather late I'm sorry to say, but FTR and FWIW, Windose really, really likes double-quotes around its command line arguments (tested on Win7):

c:\@Work\Perl\monks>echo Bleach='^(GUI_|AA_|myMainScript)'
'AA_' is not recognized as an internal or external command,
operable program or batch file.

c:\@Work\Perl\monks>echo "Bleach='^(GUI_|AA_|myMainScript)'"
"Bleach='^(GUI_|AA_|myMainScript)'"

c:\@Work\Perl\monks>perl -le "print qq{>>$ARGV[0]<<};"  Bleach='^(GUI_
+|AA_|myMainScript)'
'AA_' is not recognized as an internal or external command,
operable program or batch file.

c:\@Work\Perl\monks>perl -le "print qq{>>$ARGV[0]<<};"  "Bleach='^(GUI
+_|AA_|myMainScript)'"
>>Bleach='^(GUI_|AA_|myMainScript)'<<
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