Names.nsf probs after upgrade from v 4.6

[spi200]

Hi all

I did an upgrade from v4.6 to v 6.5 today, but after I had copied over my names.nsf to the new server it still had the old look and feel of Domino 4.6 - Our support guy pointed me in the direction of apply the pubnames.ntf template to the old names.nsf - all looked good and it had the nice 6.5 look and feel, but when I went to access the web server with some test users - no access was possible. It seems as apply the pubnames template removed or changed the Server access groups - I reviewed the setting but could see no problem with the access groups so I rolled back to my v 4.6 names.nsf and access was OK again.
I still need to get the names.nsf updated, so I was wondering has anyone had this sort of problem before.
For the upgrade I copied the v4.6 names.nsf to a working 6.5 server which was built\upgrade using an old copy of the names.nsf- I then ran ncompact,nupdall and nfixup on the names.nsf - its only when I apply the 6.5 template (pubnames.ntf) that I run into problems.
Any help would be appreciated.

Dave