Unfortunately, Linux does not have native (in kernel source) support for the exFAT filesystem (required for a device to be labled SDXC). As soon as such a filesystem is supported in Linux, we can enable direct support for exFAT.
In the meantime, there is nothing preventing you from formatting the card in a filesystem type that is supported on the target. FAT32 is unfortunately the most portable, accessible format, of course if you don't need to access the contents of the card from a Windows machine, you can use some of the tools on the RT controller to format the card in a more robust, journalling filesystem such as EXT4.
I switched to EXT4 file system and start using some windows tools for formating and read the sd card.
But i think there will be more cRIO users running into this problems. Using a Windows PC for developing LabVIEW Code and using Linux cRIO with Linux File Sytem.
And there is no note in the system spec about the file system format of the sd cards.