innobackupex makes server unresponsive during backup

Just implemented innobackupex for creating backup of about 20 databases. Works well, however I’m finding that the MySQL server becomes unresponsive during the backup process using this command (which takes about 5 minutes to complete)

innobackupex --no-timestamp --compress --user=username --password=password /path/to/backup/

I was previously using more threads, but this seemed to increase the speed with which the server became unresponsive (although that may just be a general impression). The general server load is not high. It may be connected with backing up a large MyISAM table with approx 8GB of data in it, although that’s also a bit of a guess.

Are there any common gotchas which would cause the server to become unresponsive in this way?