Actually, there could be a HUGE difference between the 97 and 00 ECU's.

I have a 96 EX and was trying to diagnose a timing/rough idle/bad gas mileage problem. The next step was to try and swap ECU's with my girlfriends car, which is a 2000 EX. The computer in her car was less than half the size of the one in my car, and I know there are minor differences in the D16Y8 engine between my 96 and her 00.

I decided not to even attempt the computer swap to test out my car, simply based on the computer size and slight engine differences between the cars. Didn't want hers running like crap too...

The dealer should definitely be able to tell you if they're different enough to cause this, but I would think that you DO want an ECU for the 00 engine, if you didn't get the right one.