I recently acquired an Nvidia Shield Portable android gaming platform, and quickly purchased a new 64GB microSDXC card from Kingston to store my portable game library. Unfortunately, as of present (Feb 17th 2016) the Shield's support for large capacity SDXC cards is somewhat limited, but thankfully there is a simple fix.
Contrary to Nvidia's own guidelines on the matter, the Shield Portable works best with cards formatted to FAT32 with a sector size of 2048KB.
1. Download GUIFormat, located here: LINK
2. Insert your SDXC microSD card into a compatible USB reader
3. Open the program and select the 2048 sector size, and format the card.
4. Enjoy your working high capacity microSDXC card!
After using the program, my card worked perfectly in the Shield Portable. I highly recommend picking up a large capacity microSD to take full advantage of the system, but you can always buy a 32GB microSDHC card to avoid the hassle.