Had this same problem sprout up at another client's site.  They were migrating from their corporate domain to a new private sub domain, and when the server moved from one domain to another the server config tool no longer worked.

I was able to track down the problem to the com+ services that were registered to run as the domain admin account that is created during setup.  I tried manually moving the accounts to the new accounts in the new domain, to no effect.

The odd part was that the old domain was still accessible via a trust, so the accounts themselves should have been allowed to run.  To make things work again I took the following steps.

1> Remove the server component of AAC.

2> from dcomcnfg remove all references to the citrix AAC.

3> Reinstall the software with the new account pointing to the same database.  Match all the names for the setup as possible.

4> Install the patch if it was installed previously (necessary.)

5> Restore the Database from a SQL backup.

6> Redeploy the Logon point.

7> Change permissions for policies to new domain.

This got the portal back up and running with the same software and configuration as before.  Grand total of time for this process, about 15 minutes, so much faster then the current fix of rebuilding the machine from scratch.