Cloned Raid Array won't boot

Trueimage 9.1 Build 3718
Windows Small Business Server 2003
Dell PowerEdge SC420
WD SATA HDD RAID1.

Upgrading the disks ( Size)
Disconnected the Server from the Internet and LAN.
Connected External (SATA 300GB USB HDD )
Boot from Trueimage CD
Clone the current (75GB RAID 1) mirror to an External 300GB USB HDD Drive.
Successful according to TI
Swap out the drives and recreate the mirror.
Boot from Trueimage CD
Clone the Drives back resizing the partitions on the fly.
( Including the "Dell" Hidden partition )
Successful according to TI

Reconnect WAN & LAN - Reboot server.

Windows begins boot, logo appears and almost immediatly re-boots.
Stop error 0x00000024 yadda yadda ... ( indicating NTFS issue ? )

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That cost me the better part of 8 Hours system down time.

What was likely to have gone wrong ?
How can I diagnose / correct it ?
How do I ensure it doesn't happen again ?

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HC