ESX 3.5 Upgrade Woes

I really want to upgrade to ESX 3.5.  However, I’m not having that much luck with it.  I’ve tried 2x now, and have had the exact same experience.  So, I do the upgrade from 3.0.2 to 3.5.0.  However, after the upgrade, not all of my VMs function.  Some of them work just fine.  However, others are sitting at the command prompt saying that no OS has been found.  It’s weird because the drives are attached and recognized, but it doesn’t like to boot from them.  It’s like it can’t find the MBR. 

Things I’ve tried to fix this:

• Analyze the differences in the VMX and VMDK files between the machines that are working and aren’t.  This hasn’t given me much as there isn’t any difference.  The only difference I noticed was in the VMDK files.  The ones that booted correctly listed the “ddb.toolsVersion”.  The ones that hadn’t booted listed it as “0”.  Sadly, changing this didn’t fix anything.
• Mount the non-functioning disks on working VMs.  By doing this I was able to view the contents of the disks just fine.  And amazingly, sometimes after doing that, the original VM actually booted.  However, they are very flakey and sometime revert back.  There is a lot of chkdsks going on on bootups too. Nothing is ever found, but it seems to always run.

I really don’t know what to do at this point.  I know that I can downgrade again to 3.0.2 and it will work fine.  The machines will boot right up without issues.  However, to downgrade, that means I have to recreate all of my Virtual Machines again.  Not completely awful, but time consuming.  I may try to do a full install instead of any upgrade too, see if that works.  Any other ideas?

I’d really like to move to 3.5 as it has some nice features.  Plus I’ll be sitting the VCP class soon, which will be on 3.5.