That pl_auto_file doesn't include any further arguments, so that's why they're disappearing. I'm not at a machine where I can show you what it should be, but...

pl_auto_file="c:\...\perl.exe" "%1" %2 %3 %4 %5 %6 %7 %8 %9
[download]

or

pl_auto_file="c:\...\perl.exe" "%1" %2*
[download]

Or something like that.