I have had similar problems with Perl scripts in the Startup folder. I think it might have to do with certain environment variables (like PATH) not being properly initialized, because the following worked for me. Caveat emptor: I haven't thoroughly diagnosed this; the fix below fixed it, and I didn't investigate any further, YMMV.

@ECHO OFF
REM -- this is a .CMD script named 'C:\sperl.cmd' to launch Perl at st
+artup.

set PERL_BIN=C:\Perl\bin\perl.exe

echo == %1 >> C:\startup.log
%PERL_BIN% -w %* 1>>C:\startup.log 2>&1
[download]

This is called like:

C:\sperl.cmd C:\path\to\script.pl and some args
[download]

A file named C:\startup.log is appended to: I have a logon script that erases this file before the Startup folder is ever executed, so you'll have to address that issue as well.