To get it to work with my 64gb cards, I use the Minitool partition wizard. Make sure you have the cluster size set to 64kb. I also had that problem lol.
I can buy a 32gb Micro SD card on Amazon right now for $20
With this price cut the 32gb Vita memory card is $80
Sony needs to either price cut the memory cards a lot more or ditch it all together in favor of SD cards.