Level-up skill developed a bug

I have started a new project and did my usual of constructing a small segment, testing it, saving and moving on once everything seems okay.  Today I decided to start a new playthrough to make sure that it all flows smoothly together.

I am using a script by DuncanS which allows skills to level up with use; each time the skill is used it gains one AP.  The script can be found here:  http://pastebin.com/raw.php?i=URF9X8cp

On my first playthrough this script worked perfectly.  This time, however, the skills start at level 3 instead of level one, and I have no idea why.  The skills have not been used, so there is no way that AP could be being added to increase the level.  

No new script has been added since the very beginning except this one: http://forums.rpgmakerweb.com/index.php?/topic/20500-gumps-level-up-messenger/.  I have tried disabling it, but it makes no difference, so I do not think that this is the cause.  DuncanS's script does not use switches, so it is not being affected by new switches I have made.

In case it is of any use, here are all the scripts I am using.

Does anyone have any idea what might be causing this?  I have constructed my whole skill system around having this script working, so it's important to me to get to the bottom of the problem.

Thanks.