This is normal with the TSM Windows client running on W2K, starting with V4.

A whole bunch of files in \system32 (all .dlls, most .exe's) are tagged by
Microsoft as "System File Protected" files.

These are excluded from the regular file backup, because you aren't supposed
to restore them individually.
The ARE included in the "system object" backup, under "system files".

If you backup both the LOCAL drives AND System object with the GUI, you will
get everything.
The scheduler does the System OBjects, including "system files" by default
when you schedule an incremental, so this causes most people no problems.

The Microsoft "system protected" files thing and the way TSM supports them
are described in one of the Redbooks you can get at www.redbooks.ibm.com:

Tivoli Storage Manager Version 3.7.3 & 4.1:
Technical Guide SG24-6110-00

Look at chapter 6.  TSM Windows Client Win2000 support.