Hmm I'd say you may need to reboot sadly. Stupid but did you just try stopping them then starting as apose to to just waiting for the restart to complete.
As there is no console to access ESX3i server's making troubleshooting difficult, reboot might be only solution. I'm assuming this is a single server?
ESX3i although free, is aimed to be used in the enterprise where clustering features of VMware's ESX products are implemented meaning you could just MOVE the running virtual machines else where, then reboot the server with the problem.
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