Thanks for the VI Mangus,
From investigating the behavior, I'll help describe what is happening with your system to give a better understanding. When power is cut at some future time, anything thats using a FAT file system can and does become corrupt if its not properly shut down. So, as you have seen, when your application loses power, if the SD cards have not been un-mounted properly, then when we attempt to mount the Card, the software sees that the FAT file system has become corrupt and requires a run of chkdsk to recover it before we can mount again.
Now, this is different than some other OS versions, as others (Windows, etc.) are more lenient on the mount side. There are lots of minor corruptions that they are lenient enough to mount anyway. NI had an explicit desire to be strict and not lenient in these cases as if we mount filesystems that are corrupt in this way we might be overwriting any data that your application may have generated. So, currently, a proper system should have a way to provide a safe shut down procedure so that File IO can have time to close and un-mount the SD card. This could be done with an external battery on the input and monitoring on the RT controller on which Power Suppy Input is being used. See the Tutorial <a href="http://zone.ni.com/devzone/cda/tut/p/id/6546" target="_blank">Designing High Availability Systems with CompactRIO and Compact FieldPoint</a> for some more information on this subject.
We have considered providing a method to explicitly Mount and SD card even though its a little bit corrupt so please file a product suggestion if you would like to see this feature.
Let me know if you have any questions.
Thanks,
Basset Hound