If you do have a problem using the library with the ATmega644, let me know. There's specific defines in the library for that chip so it should work. But, I don't have one to test so if there's a problem I'd like to know.
I just tried it on my 644P based board and just using a O-scope and one of your example sketches I could see the clocking on two pins. Different pins then what your library states, but I'm using a Bobuino pin 1284P/644P mapping scheme rather then the older standard Sanguino pin mapping, or whatever ever pin mapping you may have used as you developed the library. As there is no 'official Arduino' pin mapping defined one needs to be able to backtrack to the port/pin number used by the various timers sometimes.
Anyway thanks for adding the 1284P/644P support.
Lefty