This is a bit of a shot in the dark, but just try opening STDIN and STDOUT (and perhaps STDERR) to a dummy file and see what happens:

open(STDIN, "<c:\\foo");
open(STDOUT, ">c:\\bar");
[download]

I bet IPC::Run is expecting them to be defined, and from what I read about wperl these file handles are not initially available.

I'd be interested to know if this works or not.

Another option is to use the ->as_debug or ->as_canon method to get the input that will be passed to the GraphViz command (dot or whatever) and invoke the command yourself.