I had exactly the same problem with Windows 8, and found a fix.
Windows 8 (and 7 it seems) has an issue with reading USB drives formatted in FAT, FAT32, or exFAT by OS X, and also cannot reformat USB drives formatted by OS X to their full capacity. Windows’ Disk Management app could not even repartition the USB drive correctly.
A SanDisk supprt page for an unrelated Windows 7 formatting problem reccomended to use an application called “HP USB Disk Storage Format Tool.” I used this application on the Windows 8 computer that could not properly format my USB drive and it quicky fixed the problem, back to 64 GB from 200 MB.
A search for the application will turn up several sites where it can be downloaded.
