Despite my sincerest efforts, a bug was included in the original release of Matrix Mod Reloaded that made the mod unplayable. It has since been updated, but if you downloaded it before it was, you can download a patch here (http://www.frpmods.com/files/Conduit/matrixmodreloaded/matrixmodreloadedpatch.rar).
EDIT: Patch has been updated to take care of the second problem.