I would say both have been altered then.

Every Honda engine number wether it be NSR250, NSR500 or even RC45 will read, eg's of the above, MC16E, NSR500E and RC45E.

You will note your engine number is missing the "E". Going by the fact they marked all NSR250 engines MC16E and yours not having the 16 or the E would maybe me look very hard at the bike.
_________________
If I have to take the carbs off once more...