Terminal server is a giant security hole allowing all sorts of great local user exploits (such as emailing evil.exe to yourself and executing it) -- I really can't blame your sysadmin if he is smart enough to know the fault is in Terminal Server and not Perl.

Give me a terminal server account with simple "run programs in my account space" access, and I can bring your server to it's knees (I'm talking data loss and hardware damage -- yes, I can code to the Win32 API & DDK). If you have technically competant but disgruntled employes, for instance in a Call Center / CRM situation, you want to lock down as much as you can.

Of course, the first thing I'd do would be remove Windows and switch over to a remote-login (Linux/Unix/BSD) and thin-client type environment (Windows+Exceed or Linux/Unix/BSD)...and this is what the better shops do.

If you just need to install your apps on these servers, perhaps you can compile them to EXE with PAR and that might appease your sysadmin.