First, I would run a simple file test to make sure your script can see the file, something like

unless(-e "yourscript.bat") {
print "Cannot see yourscript.bat...\n";
}
[download]

Then, a simple system("yourscript"); call should work. Also, if your .bat script writes output, try redirecting it to a file eg. system("yourscript > out.txt");Please post the relevant sections of your code so we can be of more assistance.
-Jason