Normally I click on a perl script and it calls a 2nd script, successfully passing args via qx() and successfully getting the output.
I also tried simply typing in the name of the script to a cmd window and put the args after it. The script did not see the command line args.
Have you tried running your second script as "perl script.pl arg1 arg2 ..." instead of "script.pl arg1 arg2 ..."? You might need to add the full path to the Perl binary, which you can normally get from $^X (or Config's $Config{perlpath}, as documented in the first link). Also note my node here in regards to the potential issues with using qx//.