It depends on the timelimit set in the server's PHP setup. They can mandate that a script not run for more than X number of seconds. So when it hits that point the script stops running.
They do this so someone doesn't start a script running on the server that runs for days and uses resources.
Last time I backed you up - I had to do the tables separately - particularly the w3t_Posts table which was about 30 MB (about 44,000 lines (posts) ) and that is probably approaching the limit.
Don't really have any idea of how it can be automated given the limitations on your server though.