OK, i think i know where the issue is.  
If you look at this page:
updating_401.php
we have added additional steps when upgrading from 4 to 4.0.1.  Basically step 6 was added which was not there before.  Please try overwriting your webassist/plugins folder with the webassist/plugins that is located in the install folder of the 4.0.1 zip file.  This include the fix to your issue.
I hope this help.


