If you were to look back over the threads detailing the development and release history of Ghost 3, Symantec have never made a secret of the fact that the releases would be staged. Users were crying out for some basic updates to the core files which form the hub of the new release, but there is a lot of ongoing development work to add functionality based on user feedback, much of which was received during the public beta testing that preceded the release.
In respect of your cloning activities, are you deploying an old image created under version 2.5 or is this a new image created under Ghost 3.0? Has the operating system changed in the new image? Although the bioses may be the same, are the settings the same also? For example, is AHCI enabled for the hard disk(s) or are the bios settings for compatibility mode? This would naturally affect the requirement for WinPE to have the appropriate SATA drivers installed. In your testing, are you getting consistent results with the machine inventory - ie, do the same machines always fail, or is pass/fail a random distribution?
At this point, I would suggest giving Symantec support a call so that you can discuss your problems in more detail.