SMS 2.1 Duplicate ID’s

I just upgraded an SMS 1.2 site to 2.0 SP1 w/client hotfix and am having a problem upgrading clients. Several of them install the windows manager but no agents. It turns out they have an ID already in use by another client in the site database. Is there anything I can do about this? I’ve tried removing the client software including registry keys and the same thing keeps happening.