I'm still unclear what the problem is. What exactly is it that you are trying to do with regards to permissions? Give general example please.
A FAT formatted USB will not accept setting permissions like an Ext4 (Ext3, Ext2) formatted volume. All users should be able to read and write to the USB stick by default if it's formatted with FAT32 (FAT16, etc.).
As for files disappearing from view? It's possible that they are ending up in the Trash folder on the USB stick instead of actually being deleted, which might explain why you say the number of files being reported on disk doesn't change.
Plug USB back in, open file manager and navigate to USB stick. Type Ctrl+H, or click View -> Show Hidden Files. Look to see if there is a hidden folder (likely) called ".Trash-1000". If there is, just go to your Trash bin (probably shown on left side of Thunar) and empty the trash (File -> Empty Trash). That should get rid of the stuff in ".Trash-1000" on the USB stick as well as other things that ended up in trash from other deletes you've done elsewhere.