Why does OS X now think I have two partitions on my external USB drive (plus random connection issue)?

I have an external USB drive that I have plugged into a USB hub, which gets unplugged from my computer about once a day. Most of the time I remember to unmount the drive before disconnecting so that I don't break anything. Sometimes I forget and get the message about "usb drive disconnected unexpectedly" (or something similar).

About the drive: it is a 1TB usb-powered Western Digital drive that I use for Time Machine and other misc. documents. The drive is encrypted with FileVault2, which I think was done automatically when I told Time Machine to use it (my system drive uses FileVault2).

About the OS: OS X Mountain Lion 10.8.2 (can't say issues started w/ any recent updates, but does seem to fall somewhere within install time periods of 10.8, 10.8.1 and 10.8.2 installs)

Recently, this drive has not been showing up every time I connect the USB hub. Yesterday I noticed that the last Time Machine backup was a few days prior. Last night I waited to plug it in until my computer was out of sleep, and this time I switched to a different port on the USB hub. The drive mounted without an issue.

Today, I went to unmount the drive (via right-click on desktop), and got a message: "My Passwort" is a partition on a disk that has 2 partitions. Do you want to eject "My Passport" only, or both partitions? ....

When I go to OS X Disk Utility, there is only one partition showing under the drive.

Q1: any ideas why the drive not showing up every time I connect over the last few months (sometimes it does, other times it didn't)?

Q2: why does the OS think there are two partitions?

Update 2: Ran diskutil list, got following result:

/dev/disk0
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *128.0 GB   disk0
   1:                        EFI                         209.7 MB   disk0s1
   2:          Apple_CoreStorage                         127.2 GB   disk0s2
   3:                 Apple_Boot Recovery HD             650.0 MB   disk0s3
/dev/disk1
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                  Apple_HFS disk0s2                *126.9 GB   disk1
/dev/disk2
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:     FDisk_partition_scheme                        *32.0 GB    disk2
   1:                  Apple_HFS mini32gb                32.0 GB    disk2s1
/dev/disk3
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:      GUID_partition_scheme                        *1.0 TB     disk3
   1:                        EFI                         209.7 MB   disk3s1
   2:          Apple_CoreStorage                         999.8 GB   disk3s2
   3:                 Apple_Boot Boot OS X               134.2 MB   disk3s3
/dev/disk4
   #:                       TYPE NAME                    SIZE       IDENTIFIER
   0:                 Apple_HFSX My Passport            *999.5 GB   disk4

Update 3: As noted in my comment below, I think Mountain Lion may have installed a recovery partition on my external drive, perhaps as a secondary safety measure in case my primary drive completely dies. If this is the case, it wasn't preferred by me, so I guess take-home lesson is if you want to avoid this, unplug your externals before upgrading.

Final Update: I was tired of this message showing up, so I removed the partition with the following command (repeated for the EFI and the boot partition on my external):

diskutil eraseVolume "Free Space" Blank <DISK_NAME> # WARNING: CAREFUL WHICH VOLUME YOU ERASE!!

Q1: any ideas why the drive not showing up … (sometimes it does, other times it didn't)?

If the file system is dirty at time of connection of the disk, then the operating system will run fsck_hfs until (hopefully) repairs seem to succeed. During this period the volume will be not mounted, and the OS presents no alert.

(An alert appears only if, for example, repairs are unsuccessful.)

In your case, as CoreStorage is used to encrypt the logical volume that is used by Time Machine, there's also fsck_cs.

For your ~1 TB file system that includes backups written by Time Machine: if repairs are necessary, fsck_hfs may take an extraordinarily long time.

With Console you can browse

/var/log/fsck_hfs.log

As has been touched on, this seems to be related to Mountain Lion setting itself up for encryption or a restore partition. I found that by selecting the partition table type in Disk Utility to MBR (yuck) instead of GPT or Apple's, this behavior is avoided and one gets the extra ~200MB usable space.