Hi,
If you open the Export tileset menu, set "Tiles as seperate files" and save, it saves the files without any problem.
But if you close the window and open it again, you ll see that the last options are still there, which is also good. ("Tiles as seperate files" is selected)
But if you try to save your tileset again with that option, it does not save it as seperate files. You need to deselect and select the "Seperate files" option again.
A small bug, but it is a bug : )