DaveG:
Would it help you to report which "application parts and references" are still active?
I am not sure if and what could help you. And the best Task Manager I know so far, Process Explorer from SysInternals, shows lots of categories (open files, mutants ~ 'mutexes', threads ...) but does not have names for all parts (e.g. threads only have numbers, which are probably unique per run).
If you like, you could send me a debug-enabled client so I can return detailed reports to you. But I don't own a C compiler, I can't build one. (And please excuse, but I have to add it again: "-console" is just a useless command for the Windows client, because this console is limited in length, and cannot be redirected to a file in Windows; instead, "-logfile" would have been usefull.)
Furthermore ... I heard rumours (but won't tell names) that the 0.3.015b patch from Talad probably does not contain the same CS version you checked and reported to be fixed.