If that folder exists I would assume the install has worked ok. When you say toolbar, can you see the Archive Explorer and Search Vaults buttons??? If so then check you OWA policy (this enables/disables the horizontal toolbar buttons). Have you tried clearing your IE cache including delete files?
Failing that, you could try using the /formreg /formregmbx:(get system MB from active directory) switch with the backend2003setup.wsf cmd line. This will do a repeat forms install with the provided system mailbox.
Be interesting to see the wsf.log file if it still doesn't work after this.