I am using an RB500 r5 running Router OS 3.10 and I'm getting this output when I attempt a backup:

Saving system configuration
Configuration backup saved
echo: backup,critical error creating backup file: could not read all configurat
ion files

Anyone know what I can do here? The disk is 43% free (that's several megabytes). I'm not sure what I can try without rebooting the whole unit.

Try to upgrade the router to 3.11 version and try to perform the same operation.

On 3.11 maybe backup works - but you can't restore yours configuration on this version via winbox...

Read this:
http://forum.mikrotik.com/viewtopic.php?f=2&t=25274