When you installed Linux, did you install LILO? Assuming you did, and I'm hoping that you installed it to the superblock of the Linux partition, not the MBR. If you wrote it to the MBR, BootMagic will overwright it and you won't be bootable.
Now then, check your /etc/lilo.conf and make sure it's correct. What you're going to look for is the section that says
boot = /dev/hdxx
Which is where you need to make sure you have the right drive and partition specified.
Since Linux is on your 2nd drive, which I assume is IDE, you want boot to read /dev/hdbx which will point to the 2nd IDE drive. If you changed the Linux partitions to Primary like you said, you should be pointing to the 2nd partiton on the disk (/dev/hdb2).
Got all that? Basically, you will want LILO to have boot = /dev/hdb2, and you will also want to make sure there's a line saying root = /dev/hdb2 as well.
hope this helps a bit more.
M
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