An alternative approach, if you have the option of a build PC and a run PC, is to package your application with PAR::Packer, and so isolate it from the contaminated perl on the target machine.

In terms of multiple perls on a Windows box, make sure the perl you want to use appears first in PATH, if necessary by employing a wrapper script. This will deal with command line invocations of perl. Check the file association for .pl file types, and make sure this is pointing to the perl you want and expect.