This one was pretty interesting. Especially the fact that there is little documentation (at the time of this writing) about the selection criteria the Complete PC Backup (CPC) uses to determine what is needed for a system recovery. On my system I expected only "C" to show but CPC did also mark "D" as system and didn't allow me to unselect it.
What I found, using Process Monitor, is, that of course it scans what volumes there are and where the boot and system files are. All of this will on most Windows Vista machines be on "C". Applications and services can be on other volumes w/o CPC marking that drive as "system". I did install Visual Studio 2008 on "D:" for organizational reasons though. This got me an easy to overlook component that took quite some to time to track down as it did not show up in the procmon trace (plus the trace is not easy to read as there is no "failure" condition).
It turns out that the profiling driver (VSPerfDrv90) was added by Visual Studio Setup and referenced via the Install path on "D": (\??\D:\Program Files\Microsoft Visual Studio 9.0\Team Tools\Performance Tools\VSPerfDrv90.sys) instead of putting it into the "common" folder VS does create for some components on the system drive.
Note: The msvcmon service is referenced the same way but as that link did not cause the same effect.
So I changed the ImagePath value of the driver to point to "C" and after a reboot CPC finally showed me what I wanted.