Did you update statistics with FULLSCAN after the 2000 upgrade? It's a compulsory step.

Other than that, we'd need full table and index definitions and the actual execution plans to see for sure.

SQL Server will definitely favour scans over seek+key lookup if it estimates (using statistics) that you're returning anything over a few percent of the overall table size, as key lookups are very expensive, but a fully covering index should be used in most cases...

I'm assuming the query is actually more complicated than the example posted above, so really just guessing without the actual scenario.