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It sounds like you may have AV software getting in the way. The great increase in overall files as well as the Eclipse JAR files will kill Notes performance if they're being scanned. Make sure that you exclude everything in the Notes directory from being scanned (On Read at a minimum and potentially On Write, as well).
Are the users on relatively-modern machines?
Feedback response number WEBB8EYSJ3 created by ~James Dwowevitchynds on 03/15/2011