Have you trashed the prefs? Might be some info having been written there...
I am getting the exact same error message.
And when I check in the preferences I can't pick GPU. It worked fine with 11.0.0, but with 11.0.1 it does not work.
I even upgrade my CUDA past 4.2.7 to 4.2.10 which didn't show up in the control panel, but can be downloaded from NVIDIA's web site, but that didn't help.
And I have tried trashing both the Adobe After Effects 11.0 MC Prefs file and Adobe After Effects 11.0-x64 Prefs, and then tried the entire 11.0 folder in After Effects Preferences, but the problems continues to occur.
I just checked Premiere CS6 and it still shows CUDA support, so this does seem to be something with the 11.0.1 update of After Effects for me.
Well it was certainly the 11.0.1 Update to after effects, as re-installing the update fixed the issue.