This will be hard to crack.
Can you run app with --debug parameter and put result on pastebin.com? Start without sd card and then insert it when program already runs.
Can you also show me the partitions on this card? sudo fdisk -l /dev/sdX
And can you wipe sd card with sudo dd if=/dev/zero of=/dev/sdX bs=1M count=10 and then attaching it when program runs.
And can you try using this sd card with USB reader to see who is doing this problems (sd crd or reader).
And if you want I can build one special build for you with mode debug messages in. If you are interested...