bash script returns "out of memory" in cron, but not in shell
Even though limits.conf is commented out, I suggest that you test just to make sure. One way would be to create a cronjob that just contains something like "ulimit -a | Mail -s 'limits' [email protected]" to have the info emailed to you. Once you know what the limits are, then you can just reset them in the shell script that actually runs the rsync:
#!/bin/bash
ulimit -d unlimited
ulimit -m unlimited
ulimit -s unlimited
rsync [...]