I have experienced similar problems with Office 2000. Publisher is on a seperate CD with all sorts of 'extras' for the basic Office installation - if you have done a full install with CD2 it makes changes to the Access installation (something to do with Small Business tools?). The result is, when you double click a database you get an error message and in my case it requested Office CD1 to complete an installation. A work around is to open Access from the start menu and find your database from the 'More files...' link of the dialogue box. I have had success on a couple of machines by putting in CD1 when requested, but an additional issue is with Windows 2000 - it only works with Power users and Administrators.
Sorry about all the waffle - the bottom line is load CD1 and when the option appears select 'repair' to see if that helps.