EDIT: Answer at bottom, but my OLD card turned out to be the defective one.
I just upgraded from a Sprint Samsung Epic 4G to a Sprint Samsung S4. My S4 is already rooted and has TWRP.
To go with my new phone, I bought a Patriot Micro Mobility 64GB Micro SDXC card. The card is class 10 UHS-I and is obviously formatted exFAT. The first thing I did is format it in the phone (which curiously gave me a little bit more free space), unmount it properly, insert it in the little USB reader it came with, and then use Win7 to copy the full contents of my old SD card onto this one. The next thing I did, from cygwin, is a full "diff -rl" between the old and new card.
To my surprise a single file differs, from a single nandroid backup instance: clockworkmod/backup/2013-06-02.21.44.05/system.yaffs2.img If I do a cygwin "cmp --verbose" I see what looks like 1-bit differences, always about 240MB into this 251MB file.
If I rename that file on the SDXC card and copy it again and immediately "cmp" it, it compares fine. If I then do a full diff again, the file "changes" and is now different -- with a different number of differences from the renamed first copy. (Yes, those two files differ from each other on the SDXC card.) I can do this as many times as I want, getting the same behavior each time. Once I get differences, it doesn't seem to change again after that. My guess is that it is corrupted on copy but when I do the first "cmp" I'm not reading from flash but reading from the Windows file system cache. And that the full diff effectively flushes that cache so I see what is really on the flash.
EDIT: After much painful investigation, I discovered that it's not the new 64GB SDXC card that's defective. It's the old 32GB SD card that is defective. Only one file gets corrupted when copied off of it. I took the new SDXC card out of the picture by copying the one bad file to my hard disk, then unmounting the SD card, then remounting, then again copying to my hard disk (different filename), then repeating. I get different file contents every time I do this. This happens even with different USB readers.
I've never heard of such a thing, but this card is two years old. Looks like I need to make one last nandroid backup of my old phone, since this one gets corrupted when copied off the SD card!
If anyone has seen anything like this before, I'm still interested in hearing about it.