Moron, can you please post a minimal test case, which illustrates the false differences.

Also, I'm interested in whether Algorithm::Diff suffers from the same problem, as I have quite a bit of code depending on this module. No doubt the author of this module would also be interested if it is failing.

In terms of a cross-platform pure perl diff, I include a script for this in my module VCS::Lite, called vldiff.