The problem turned-out to be with the vst plugins. Go to your Program Files folder (it will be Program Files (x86) for Cuabase 32 bit in a 64 bit version of Windows. Open the Steinberg folder, open the Cubase 6 folder, open the VST3 folder. There is a file called Cubase plug-in set.vst3. This is updated with each version of C6. 6.0.0 has a file dated 26 Nov 2010 (on my DVD), the 6.0.1 update has one dated 28 Feb 20111 and the 6.0.3 update has one dated 30 Mar 2011. My problem is with the 30 March dated file. Either of the older folders fixes the problem. If you have .0 or .1 installed, copy this file somewhere safe, do the update then replace the newer file.
More details here http://www.steinberg.net/forum/viewtopic.php?f=19&t=8009