To protect from conflicts between Windows NT, 2000 and XP, System Commander automatically hides all primary NTFS partitions from the one you boot to. This may or may not be what you desire.

If you store data in a non-booting NTFS primary partition, the partition will be hidden by default.

You can control partition hiding from the Settings, Specific OS Options menu.

If you only have one NT/2000/XP and do not plan to add another, it is safe (and maybe even necessary) to unhide all NTFS primary partitions. To do this, at boot time, select Settings, Specific OS Options, under the Partitions Visible/Hidden area. Double click inside the "Drive-0" box, this will bring you to the Access Control screen. There you can change which partitions you would like visible on Drive 0. If the primary NTFS partition resides on Drive 1, then change Drive-0 to Drive-1 before double clicking inside the drive box.

Why does System Commander default to hiding NTFS partitions?

There are 3 different NTFS formats currently in use, as follows:

NTFS Version Understood by Windows 
3.1 XP and 2000 SP3 and later 
3.0 2000 and NT SP4 and later 
1.0 NT 4.0 and older

This means older OSes (NT with SP3 and Windows 2000) do not understand the latest NTFS format. Similarly, Windows XP and 2000 uses an version that Windows NT does not understand.

Windows XP will convert any NTFS partition it finds into the latest NTFS format. If you have either Windows NT SP3 (or older) or Windows 2000 installed into a NTFS partition, XP will destroy the ability to boot those older OSes. The operation is not reversible, but the partition can be read or written by Windows XP.

When you run Windows 2000, it automatically converts any NTFS partition it sees to its NTFS style. Should you have Windows NT installed in a NTFS partition, this will destroy the ability to boot NT, and the operation is not reversible. You can still read or write the partition from Windows 2000, and in some cases NT.

Unfortunately, Windows will not warn you of the conversion, nor are there any options in Windows to prevent this. System Commander hides these partitions in a special way that prevents newer Windows from changing version of NTFS partitions. This allows you to safely have Windows NT, 2000 and XP all on the same system.