by David Rogers.
I was running into a similar issue. It turns out that apache was running php as "FastCGI," which has its own group of timeout settings above and beyond the normal php settings..
I found one setting in particular, FcgidBusyTimeout, that was set to 90 seconds. Anything that took longer than 90 seconds to complete was killed and failed.
Bumping FcgidBusyTimeout in my php.ini from 90 to 300 enabled backups to work for me. Perhaps this might help you as well?