Interesting restore problem with Alfresco

I am running Alfresco 4.2.c Community Edition on two servers. The main server and a development server. Occasionally I take the image from the main machine and restore it to the development machine.
This time when I did it my restore script remade the postgres database then copied the new contentstore over the old one. I remade the index and promptly received an internal server error once I had successfully logged in.
I stopped Alfresco.
I manually copied the files over from the backup contentstore to the live one in Alfresco and then deleted the index files as before and remade the index. It worked perfectly.
So what was the difference between using command line and manually using Dolphin?
I may try to delete the directory before copying over.
I suppose it is another mystery to solve.