The problem I was having was with my Test environment. So I thought that I would do the upgrade in my Production environment so that when the problem occurred there, I would only need to log the one support call. I initially had another problem which was with insufficient disk space - see the following link for how that was resolved http://communities.vmware.com/message/1990409#1990409 - but after that was sorted and the upgrade completed I was amazed to discover that everything just worked. I didn't even had to run the script on the DB. I did have the "500" error when I went to the reports tab, but after clearing that once, the reports page displayed and everything just seems to be working perfectly. What is disappointing here is the inconsistency of the product. The 2 environments that I have are setup exactly the same using the same versions of vCenter, ESX, CapIQ and vCops. I have even tried the upgrade in my Test environment again (for about the 20th time) and this time I added my disk space just as I had done in the Production environment, but this time things seemed even worse. I will still log a call with Tech Support, but I'm resigned to the fact that I think a clean install in my Test environment will be the end result.
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