NB: This is all guesses. I haven't proved any of it.

I believe you're saying "When I run this command with *this* argument, the argument gets mangled"

Short Answer (I think, not tested at all):

system("VisualSourceSafe", "history", $variable);
[download]

Long answer: you're giving system 1 argument, which contains a "special" character, so system hands it to the shell for processing. Passing system a list avoids that problem.
Check perldoc -f system for more information.