it appears as if the MsTimer2 lib hadnt been updated for the new hardware, the changes were trivial
http://updatelee.com/src/MsTimer2.cpp.patch
hopefully someone can look that over and confirm its all good. It does work on my 2560
What software can I use to apply this patch to the original MSTimer2 or better yet, do you have a link to where I can download your modified .cpp and .h files?
Thanks!