I managed to regenerate the tables for all my databases upon upgrading to IJC 5.5.1, except one. Here I am not allowed to log in as administrator anymore, as witnessed by the attached error message.
this probably means that last user in IJC 5.5.0 weren't successfully logged out from the IJC schema.
There is a workaround. Use your favorit SQL editor (e.g. MySQL Workbench, phpMyAdmin ...) and find the table ijc_user in the affected database schema. Delete all rows in this table.
You should be able to acces IJC schema with admin rights now and subsequently update tables...
The description in dialog is a bit confusing in this case. We will correct it in future release.
This is going to be solved in the IJC 5.6. New dialog box would provide correct information.
If it tells you that someone is logged in and actually is not (application was badly ended and information about last logged user just remain in database table...), than it's possible to try log in as last logged user. This should remove the lock in database if table upgrade is needed. After this you can log in as admin and start to upgrade JChem tables.