yamaha 200 hpdi problem

[jp3731]

I have a 2001 200hp hpdi on a 24ft bay stealth. Two years ago I had two cylinders blow. The dealer said it was because of water in the fuel. I had the power head rebuilt and yamaha supplied the parts I paid for the labor. They changed to the higher micron filters at this time. When they pluged in the computer it said the engine had 6500 hrs. on it. As I am the original owner I know this isn't correct I estimate there is no more than 200 hrs. Yamaha would not replace the computer even with this obvious error. Two days ago I blew out no. 1 cylinder. This time I have been diligent on fuel quality so this shouldn't be an issue. The Yamaha tech did not offer a reason for this failure. My question is could a bad computer cause this problem?