Conflict with backupbuddy

I’m running wp super cache and everything is fine apart from backupbuddy, which throws this message

“One or more caching plugins were detected as activated. Some caching plugin configurations may possibly cache & interfere with backup processes or WordPress cron. If you encounter problems clear the caching plugin’s cache (deactivating the plugin may help) to troubleshoot. Activated caching plugins detected: WP Super Cache.”

And sure enough when I try to back up, after a few hundred megabytes backupbuddy fails and throws me an error. What should I do to get backupbuddy and wp super cache to work?

Thanks

http://wordpress.org/extend/plugins/wp-super-cache/