In the end I came up with the following solution - but it only works for windows users so you chaps with nice shiny Macs will have to use something else...sorry!
Select and copy the following line:
FOR /R "c:\Working" %%a IN (CaptureOne) DO RMDIR /S /Q "%%a"
Open Notepad and paste in the text
c:\workingwith the name of the directory where you keep your photos;
C:\Documents and Settings\Chris\My Documents\My Pictures
Save the file as C1.bat on your C: drive.
Now when you double click on c1.bat in Explorer, all the Capture One temporary files will be removed as if by magic.