Karsten you're probably right. We've not tested on that old MySQL. We will fix this. You can just remove these comments from the SQL files and it should run fine.
Shouldn't MySQL just skip that /*!40000.....*/ line?
I don't know the meaning of /*!40000 in great details, but I thought it meant something along the lines of: "don't execute this, unless the mysql version number >= 4.00.00"