Problems with NITDroid
 

Earlier when i used NITDroid, all of my files in MyDocs have been deleted after every reboot. Every time, i only found Android's folders, which makes me suspect that Android deleted them.
This makes me not want to use NITDroid, but my question is:
Is there any way to make Android not do this? Or possibly not access MyDocs at all and use the FAT-partition on the memory card instead? I value my files over having Android.