I think one of the problems was that I somehow deleted one of the block directories (the html block), and when the database couldn't find it it came up with a fatal error.
Also I checked out a completely new copy from CVS.
Also, there were a number of empty directories checked out from CVS such as mod/resource/type/reference, mod/resource/type/program, and lang/sr with I had to delete to get the menus working properly.
Thanks a lot to Jon and Daryl for offering a hand,
Cheers, Tim.