in the absence of info heres a couple of guesses.
1) are you sure its a ISAM table and not a MyISAM table? its curious that you're not able to run isamchk even after recreating the database.
2)is there any pattern to the deletion?
3)if you're logging all of the sql commands sent to mysql, have you checked the log (default location is /var/lib/mysql/ on my box) for any sql deleting rows that you know should not be deleted?