Alright, this is a bit funky. First of all, contents of /media before the reboot (I had manually cleaned it up to look the way it should since it was full of junk directories from previous mount points):

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$ cd /media
$ ls -l
total 44
drwxrwxrwx 1 root root  8192 2008-03-27 20:12 Archive
lrwxrwxrwx 1 root  999     6 2008-03-29 06:15 cdrom -> cdrom0
drwxr-xr-x 2 root  999  4096 2008-03-29 06:15 cdrom0
drwxrwxrwx 1 root root 16384 2008-03-27 20:12 Data
drwx------ 4 user root 16384 1970-01-01 01:00 disk
drwxr-xr-x 5 user user   104 2008-02-25 17:42 disk-1
---

And now after the reboot:

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$ ls -l
total 60
drwx------ 2 root root  4096 2008-04-04 21:02 Archive
drwxrwxrwx 1 root root  8192 2008-03-27 20:12 Archive_
lrwxrwxrwx 1 root  999     6 2008-03-29 06:15 cdrom -> cdrom0
drwxr-xr-x 2 root  999  4096 2008-03-29 06:15 cdrom0
drwx------ 2 root root  4096 2008-04-04 21:48 Data
drwxrwxrwx 1 root root 16384 2008-03-27 20:12 Data_
drwx------ 2 root root  4096 2008-04-04 20:48 disk
drwx------ 2 root root  4096 2008-04-04 20:48 disk-1
drwx------ 4 user root 16384 1970-01-01 01:00 disk-2
drwxr-xr-x 5 user user   104 2008-02-25 17:42 disk-3
---

As you can see the old directories from the last session are still there, albeit with changed permissions/ownership, unaccessible to the normal user and with nothing mounted to them. The ones now mounted are Archive_, Data_, disk-2 and disk-3. These are the symptoms of this bug that I initially encountered / was aware of.

Now, trying to run the same gnome-mount command from last time revealed this:

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$ gnome-mount -vnbtd /dev/sde1
gnome-mount 0.8
** Message: Given device '/dev/sde1' is not a volume or a drive.
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Weird. fdisk further reveals:

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$ fdisk -l

Disk /dev/sdc: 160.0 GB, 160041885696 bytes
255 heads, 63 sectors/track, 19457 cylinders
Units = cylinders of 16065 * 512 = 8225280 bytes
Disk identifier: 0x00013b82

   Device Boot      Start         End      Blocks   Id  System
/dev/sdc1               1       18156   145838038+   7  HPFS/NTFS
/dev/sdc2           18157       19456    10442250    f  W95 Ext'd (LBA)
/dev/sdc5           18157       19456    10442218+   4  FAT16 <32M

Disk /dev/sdd: 500.1 GB, 500107862016 bytes
255 heads, 63 sectors/track, 60801 cylinders
Units = cylinders of 16065 * 512 = 8225280 bytes
Disk identifier: 0x8d399bc0

   Device Boot      Start         End      Blocks   Id  System
/dev/sdd1               1       54235   435642606    7  HPFS/NTFS
/dev/sdd2           54236       60801    52741395    b  W95 FAT32
---

What used to be /dev/sdE1 is now /dev/sdC1 (along with changes to all other device names). 

Running gnome-mount on the new device name shows this:

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$ gnome-mount -vnbtd /dev/sdc1
gnome-mount 0.8
** (gnome-mount:6766): DEBUG: Mounting /org/freedesktop/Hal/devices/volume_uuid_F09C547A9C543CF2
** (gnome-mount:6766): DEBUG: read default option 'locale=' from gconf strlist key /system/storage/default_options/ntfs-3g/mount_options
** (gnome-mount:6766): DEBUG: read default option 'exec' from gconf strlist key /system/storage/default_options/ntfs-3g/mount_options
** (gnome-mount:6766): DEBUG: Mounting /org/freedesktop/Hal/devices/volume_uuid_F09C547A9C543CF2 with mount_point='Data', fstype='ntfs-3g', num_options=2
** (gnome-mount:6766): DEBUG:   option='locale=en_US.UTF-8'
** (gnome-mount:6766): DEBUG:   option='exec'
** Message: Mount failed for /org/freedesktop/Hal/devices/volume_uuid_F09C547A9C543CF2
org.freedesktop.Hal.Device.Volume.AlreadyMounted : Device /dev/sdc1 is already mounted.
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Which, as far as I can tell, is exactly the same except for the "already mounted" error message at the end which I already mentioned previously. If I manually unmount that partition first, it should look exactly the same. With the exception of the new device name of course. Will reboot again shortly to see if the device names change again.

By the way, is just pasting the output here alright or would you prefer I save it to a text file and add that as an attachment?