That helps. Sometimes larger courses are hard to back up. You might try raising the time out limit in your mysql config file - that might help. (Probably called my.cnf depending on your setup) Or, if 2.5 has the experimental new backup format, try turning that on (can't remember when that was introduced). Backup performance has improved a lot with later releases - an upgrade might help.
If all else fails, you might try backing the course up in halves or quarters. A pain, I know, but sometimes necessary.
When I have seen that error before, it is sometimes accompanied by more detailed info as well. Questions are often responsible for backup issues and the details will sometimes point you to the specific questions that are causing the issue.
Backup and restore
Moodle 2.5.1: Backup Course "Internal Server" occures
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