A general question regarding Dell EISA FAT16 file

Hello, We have a problem with a recent Acronis Backup and Recovery 10 product (I mean an operator problem) that we installed at a customer site. I’m at home today so there are a few details missing since I don’t have access to the server, however I would like to ask some general questions so maybe by early tomorrow I can get started at the customer’s location. We’ve installed version 9 several times on clone type machines with clean HD drives and backed up and recovered with zero problems. But the machine we’re working with now is a new Dell Poweredge, Windows Server 2003 O/S and after a successful recovery we cannot boot. The backup runs just fine and the recovery runs just fine, but no boot. I assume the problem is with the FAT16 EISA file on the front of the drive. The Windows Server 2003 O/S was installed using the Dell CD. The first time I did the backup I did not check box that particular file thinking I did not need it. But when that boot effort didn’t work I ran several more backups this time including the FAT16 file but could not restore again. After including the FAT16 in the backup mix the Dell console would come up but no regular Windows boot. My question is do we have to make some manual code adjustments after the recovery, like to the MBR? If so could someone point me to the most likely change? If more information is needed I will post first thing tomorrow when I have access to the server. Thank you for any help you may be able to give me.