(near line 122 on my installation - 1.97+).
I'm not sure how those statements interact with the values set in php.ini.
I'm having the same problems with my largest courses. A course backup that I ran on just one of these large courses created a ZIP file that is 618MB. (Lots of video and audio files...)
I've changed the values in both php.ini and in backup.php (6000 seconds and 256MB) to see what happens. If I can get it to work, I'll start reducing some of the numbers to see what really fixed it.