Dennis,
Is your 2003 server 32bit, and are you running the Final Build of VC 6.1.4 ?
I have the means to test and try to reproduce this, I just need to know more about your environment.
Since VC is installed to drive C, and it was drive D that filled up, I have some concerns about other settings on the server.
Is your system's pagefile on drive D?
Any other Environment Variables set to drive D? %TEMP%, %TMP%, etc.. ?
Basically, other than storage for files of some sort, what is drive D used for. Does VC use drive D in any way via Triggers or copy jobs, etc... that rely on drive D being there?
Anything you can think of related to VC's interaction with drive D and/or requirements of the OS on drive D would be helpful.
Brian