Unable to boot from cloned MacOS 10.6.8 server

Hi there,
we've successfully restored a MacOS 10.6.8 server image to an Intel Xserve. However, there seems to be a boot cache issue. Sometimes I am unable to boot and MacOS Server won't restart. The Xserve restarts twice on the gray Apple screen. Than it's hanging on the gray Apple screen. no disk activity for minutes. I've waited 30 minutes. I had to power down the server. After that the server boots normally. no errors in verbose mode during startup.
I am using 3 volumes (all 3 using the same system clone). All Bay drives using the original Apple Disks. They are brand new. <29 hours.
Resetting the NVRAM a couple of times didn't solve the issue. The booting error is reproducible. This system runs fine and it's really clean. I just installed the latest MacOS 10.6.8 combo Update
I don't know what else I can I do? I really appreciate any help on this.

Sorry for the delay in responding.
Thank you, Peter. The Xserve running fine so far. We've had any boot issue.

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