You don't need to change it. If you are using jboss 4.0 just add your own for mysql. you can find the correct map for mysql in /docs/examples/jca. Alter that file to your own requirements and then dump it in the deploy directory.
I do need to change it because I am running an extremely memory constrained configuration and I need to save every byte I can. Hsqldb eats up a significant amount of memory that I was hoping to save.
Thanks for the link. It is very useful, but as at 4.0.1 RC1 it is incorrect for MySQL 4.1. The problem turns out to be a change introduced in JBoss 4.0.1 that 'hard codes' the Timer table column names in the EJB Timer GerneralPurposeDatabasePersistencePlugin. I have raised a bug report on it, but in the meantime the options are use 4.0.0, use the noop policy, or patch the source and build your own.
I also stumbled across this problem - Does somebody know whether it is fixed in 4.0.1rc2?
Remove jboss-media-entity-ejb.jar and start server