The problem was caused by trying to do the old trick of installing a new server then copying the data directory and notes.ini from the old server over the top of the fresh install. What we hadn't thought about was that this would bring back all the old 8.5.3 files in the workspace directory. We did it this way because we also upgraded the server's operating system from Win 2003 to 2008 64 bit and therefore could not do an “in-place” Domino upgrade.
To fix the problem we reinstalled 9.0.1 (uninstall/reinstall) and only copied the NSFs we needed from the old data directory to the new one (this included names.nsf of course).
It seems so obvious in retrospect that just replacing the new data directory with the old one would cause problems. There are loads of java files that were wiped out by us simply replacing the whole data directory.
Oh well, you live and learn! :)
Thanks for your help. It was very useful to learn of the “tell http osgi” commands.