ppm is a batch file itself. if you call a batch file from another batch file the calling batchfile ends. If you don't want that behaviour you have to call the batch using the call keyword. Hence your code becomes

:: opt_ppm_patch.bat 
:: installs ppm packages
@echo off

echo Adding the current directory to Perl Package Manager (PPM)
call ppm rep add REPOS .

:libxml_perl
echo Installing libxml-perl package
call ppm query libxml-perl 
IF NOT "%OUT%" == "No matches" goto XML_REG
call ppm install libxml-perl.ppd


:XML_REG
call ppm query XML-RegExp
IF NOT "%OUT%" == "No matches" goto XML_DOM
echo Installing XML-RegExp package
call ppm install XML-RegExp.ppd


:XML_DOM
call ppm query XML-DOM
IF NOT "%OUT%" == "No matches" goto END
echo Installing XML-DOM package
call ppm install XML-DOM.ppd

:END
echo Deleting the repository entry from PPM
call ppm rep del REPOS
echo Completed installing perl modules.
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