I was on the phone for HOURS with Adobe's tech support regarding this issue, and I was sad to say that the representatives helping me had no ability to help me except by reciting what was in their "script". They first thought the issue was with my serial number, so they were asking me to go to pull-down menus under "Help" that actually didn't exist. I think Adobe hadn't even provided them with documentation that was up to date on my version of AE and Premiere. When I asked if they could verify what they saw under their Help menu, and the version they were using, they dodged the question revealing that they actually weren't in front of a working version of the software.
That said, here's what I know:
I upgraded my motley crew of software to the CS4 suite. Support said this could be the issue, but were unable to help me find the serial number inside my software. This is because somehow our serial numbers are now somewhat detached from our software. Instead our serial number is more like a registration code on their end. The problem with this is that we had no way to tell if I was having a conflict between AECS4 standalone and AECS4 from the bundle, or which serial number my computer thought it was working under.
---IF ANYONE CAN TELL ME WHERE TO FIND MY "CURRENTLY USING" SERIAL NUMBER, THIS WOULD BE APPRECIATED. (I'm not yelling. I'm just separating out the request from the diatribe.)
They also had me log-on to Adobe for my serial number, but you may discover that this is not an up-to-date repository of your serial number. This is just a goofy virtual "post-it-note" to dig up old info. Adobe has me registered as using AE6! Obviously this database is not being used to validate my registration.
Try the usual, delete prefs, or even re-install software. And yes, if you try to work standalone-to-bundle, you'll probably have issues. You can also break the link pretty easily by moving a file or renaming anything. After finally getting a link established between AE and Prem. (imported a prem. comp into AE) I somehow broke it again. AE would hang when loading the file, and after about 4 minutes, either crash or open with a placeholder as my Prem. source, and the "Cannot establish link" warning. I just had to start over from my backup AE file that was pre-linked and try it again.
Good luck. In my experience, this is potentially a great feature that has not been nailed down by Adobe. They need to build in much smarter links that can track external changes in file structure before this will be useful.