I founf the solution:
Apparently you have to create an integrated installation.
ie One where the original \386 files are integrated with the new ones from SP1, then run winnt32.exe
Link below:
http://support.microsoft.com/default.aspx%3Fscid%3Dkb%3Ben-us%3B828930
Yes, that was what I tried the first time, the winnt32.exe file is the same version as the one on the 2K3 install CD, and I assume that somewhere there should be a newer version, but I don't know how to get hold of it.
I have completed setting up a new server, installed SP1 and other updates.
When I run winnt32 /cmdcons from the CD I get an error message about trying to use an old version of windows, but I can't find a newer version of winnt32 in the \386 folder left by SP1
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