- use a true (transactional) _DataBase_, not MySQL _and_not_ hsqldb
- have your DB on another machine
- have a recovery procedure for your DB (may last hours in case of Oracle ;-)
JBoss can not guaranty ACID if the underlying system is not able of.
If you use HSQL and the .script file is corrupted (look at the end), simply edit off the last lines in the script and restart. You can test this by using the HSQL client program to connect to the database and do a SHUTDOWN COMPACT.
Which filesystem are you using?