Yes that's correct you can't upgrade by applying SP3 or SP4. You have to completely uninstall the Exchange agent, then install using the Exchange agent in SP3, then apply SP4 to that.
I spent days on this issue and were completely disgusted that apply SP3/SP4 didn't upgrade the agent...
I had the same issue. The issue is actually due to the fact that Exchange Agent only supported Exchange 2000 from SP3 onwards. If you installed the Exchange Agent from the original CD (pre SP3) for example, it only works with Exchange 5.5 NOT Exchange 2000. Amazingly, even if you apply SP3/SP4...
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