if you had already created the tables when you installed your Demo version, you shouldn't have needed to run the createtable script when upgrading...
that being said, in some cases altertable scripts can be run out of order,
if the changes they make are not dependent on changes made in a script you haven't yet run... make sense? To clarify:
if altertable1 adds a new column to a table and altertable2 changes that colum's width (from 10 characters to 60 characters), and you try and run altertable2 before altertable1, you will get an error because the column does not exist.... Anyway, I would look over the scripts, see which altertables from 5.1.x -> 5.4.6 you did not run, verify that those changes were not made in your database, back up your database, and try running the scripts in order (minus the one you have already run...)
Remember:
ALWAYS back up your database before running the altertables!!! You could regret it if you don't!
Matt Reinfeldt
http://www.mattreinfeldt.com