Erm... afraid your wrong there... when I first heard of the NatAmi last year and visited the site 100% backwards compatibility was clearly stated on it and is the main reason why I support this project so much... 
NATAMI have *NEVER* boasted 100% compatibility. Given you are using an FPGA to mimic the chipset, you are at BEST, an APPROXIMATION of the chipset.
You can get it *CLOSE*, but if you want 100% compatibility, then use a REAL amiga.
Even Minimig, does not boast 100% compatible, and lets face it, those working on the firmware have done an EXCELLENT job, there are some titles that will *JUST NOT* run, and the same will happen with NATAMI.
Topics on Compatibility:
The NatAmi is compatible to the OCS/ECS/AGA AMIGA chipsets.
It says "Compatible", not 100%.
Like I said, Minimig is Compatible, but not 100%.
AMIGA applications, games and demos that run on classic 68060-Systems,
will run on NATAMI as long as they have not any constrains to chipset timings/limitations.
SO they have openly admitted there will be some incompatibilities, therefor, not 100%.