As far as I can see, the problem is not so much System Commander as it is in the way you actually installed Linux. If I remember correctly, you are actually given the possibility of not choosing the MBR. You want to set up a separate boot partition for Linux. I still haven’t gotten around to installing Linux on my new machine, so I can’t give you all the details. However, I’m sure there are others on the list who can.
I did have an older version of System Commander and ended up not using it for my Linux installation (I wanted to have both Linux and Windows 98 – each on it’s own hard disk. Because I had so much space on my first hard drive, System Commander (SC) absolutely insisted on preparing a Linux partition on the first hard drive – it would simply not allow me install it on the second hard drive.) I was much more successful by allowing boot on my CDROM and then starting up the installation directly from the CD-ROM – this way I was able to bypass SC. During the installation, I was able to make all the choices necessary for running a dual system on my computer. Once I LINUX was installed, I updated System Commander from Windows 98 (if I remember correctly) and Linux showed up on the System Commander menu. You may have to make a change in the SC setup (that is to say before you start any of the operating systems). If I remember correctly you have to go ‘setup’ and change ‘force partition active on drive 0’ to ‘yes’. This may, however, no longer be a problem in SC 2000.