i had similar problems before.
my problem was caused by this:
- an SD card formatted using the PC can only be mounted via /dev/mmcblk1 as fat/vfat.
- if I use linux fdisk on the SD card to create partitions, & format /dev/mmcblk1p1, then i have to mount /dev/mmcblk1p1. mounting /dev/mmcblk1 would fail.
(all above actually makes sense if you know a bit of how disk contents are written).

so, i updated some system scripts in my n900 to handle all those cases properly, including BackupMenu.
also updated scripts to recognize ext2 partitions.
attached original scripts & updated scripts (to be placed into /usr/sbin).
no warranty provided.
use at your own risk!

warning: if you don't take precautions, you run risk of bricking your n900 permanently because some partitions can't get mounted. first be sure you know how to unbrick your n900, then try.