I would like to add my support to this report.  I had similar problems.  Here is my supporting report:

Hotplug of msdos formatted Compact Flash has unexpected results after changing the "File System:" under Media Properties Volume tab Setting to msdos.

By default, the Compact Flash device is mounted as a vfat volume, and has the uid option set to my UID thus giving me full access to the device which is expected.  However, when I set the "File System:" value to msdos, then unmount, and replug the Compact Flash, it accepts the msdos file system type, but is now mounted without the uid option and hence becomes owned by root.  Although as a user I have read access to it, I can't make any changes without using sudo or launching a root terminal.  When I try to set a mount option of "uid=1000 gid=1000", I get an error "Cannot mount volume.  Invalid mount option when attempting to mount the volume." and have no apparent way to recover from this error.  The documentation doesn't help as there is no guidance about this dialog box tab.

After spending several hours exploring various man pages, Ubuntu Forums, and a lot of trial and error, I found a clue to turn on the "Applications"/"System Tools" menu, and found the "Configuration Editor".  Still with no clear guidance, I found the "system"/"storage"/"volumes" tab which contained a string with my devices UUID.  Once there, I was able to figure out how to unset the invalid "mount_options" key and get the device to automount again, but still with no write access.

While I was in the configuration editors system/storage tab, I noticed that under default options one option that is set for vfat is "uid=".  When I try to set a mount option of "uid=" in the "Mount Options:" field of the Media Properties dialog boxes volume tab, I get an error "Cannot mount volume.  Unable to mount the volume." and again am locked out and have to go back the the Configuration Editor to recover.  While there, instead of unsetting the "mount_options" key, I decided to try actually setting it to my UID, and finally was able to get the device to mount as I wanted it to.

It seems to me that any options entered into the settings for the Drive and Volume tabs should be validated before being accepted by the application, especially if the consequence of the entry will result in a need to use functionality that is hidden from the user by default.  In my case, my original purpose was to be able to use my Linux system to more easily make changes to data and configuration files on a compact flash disk that contains a MSDOS Partition for a legacy MSDOS system that I need to maintain.  I have noticed in the past that if vfat entries get written to the MSDOS disk, I get spurious errors and unpredictable operation from the legacy system, thus the need to have the compact flash disk mounted as an MSDOS partition.  My normal procedure has been to use

   mount -t msdos /dev/DEVICE -o uid=MYUID,gid=MYGID MOUNT_POINT

as root, and everything worked as I wanted it to.  As Linux has "progressed" I have noticed that the compact flash would automount, but as a vfat volume, so I would need to unmount it then go to root and mount it as before.  After upgrading to Hardy, I decided to try to find a way to either get the automounter to ignore my MSDOS devices, or mount them properly.  I found a hint about the Media Properties dialog box in the desktop forum while searching for mounting information.  After figuring out the solution to the problem asked about there which involved properly setting the "Mount Point:" setting, I decided to try playing with the "File System:" setting leading to the sequence of events described above.  While I may not be an average user of the Ubuntu Linux Operating System, I hope my experience and description of this usage problem will help to improve the operability of the desktop.