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boot record changed



I have encountered an interesting problem that I would very much appreciate any feedback on.
 
I am using System Commander with Redhat 5.0 and windows 95 on separate drives and have been successful prior to win 98.  During the win 98 upgrade, I had to completely reinstall everthing.  After SC was installed, I booted up and selected linux as usual. I opened linux and it was fine.
 
This time...when I rebooted to get back into windows, I got a message that there was no active partition or bootable HDD.
 
I then rebooted to a start up floppy and used fdisk to set the first drive (win 98) active.  I rebooted again and SC came up.  I selected win 98 and it started and ran as normal.
 
I repeated this process (reboot-linux-reboot-'no active HDD error'-reboot-set drive C active-reboot-win98) several times.  Each time I went to linux I ran LILO config to try and reinstall the linux boot info to the linux partition, and try any other options.  Nothing changed the original condition.
 
Do I need to edit the linux bootup to prevent it from wiping/altering the boot record I want?  Has anyone done this?
 
Has anyone else had the same problem with System Commander?
 
I also have Norton Utilities 3 on win 98.  It detects the altered boot record and tries to 'fix' it but keeps crashing.  Any information about boot records I would greatly appreciate.
 
Also....Linus Torvalds gave a great interview in the last Boot magazine if anyone is interested.
 
Cheers.
 
 
D.L.Grindstaff
v 612.698.5137
d/fax 612.698.5137
eMail: grindl@ix.netcom.com