<chant>without code samples it's hard to say </chant>

That said, Program B likely expects an argument to the -t switch, and is using filetoprocess for that. Check that -t requires no additional arguments that would gobble up the filetoprocess argument.

The described behavior would happen if you had a <> in your program somewhere, and in ProgramB.cgi you were shifting off two elements of @ARGV based on the -t switch.