my experience with my 16GB pendrive and two prtitions (sda1 for boot with 16MB and the rest [sda2] for my files) was that sometimes (mostly after uninstalling some tce extensions), sda2 have been remounted read-only, and then i had not any chance to write in my directories, neither as a user, nor as root; i have reformatted it fat32 with only one partition, and since i don't have any issue of that kind