[Galaxy S II Q&A, Help & Troubleshooting] Yunabeco:
I have a similar problem, though I'm not sure if it's related.

CM10.1 20130601 nightly, stock kernel; I encrypted my device fine, then found out the emmc/sdcard0 plainly disappeared when rebooting.

Completely undetected/gone from the Storage settings screen aside from the lone header, didn't manage to mount manually, and reformatting it to vfat didn't help, either.

I'll chime back if I ever find something.

EDIT: Didn't fish a lot of useful stuff out of a logcat, unfortunately.

It pretty much fails to find a FS on the Vold block device and gives up. Flashing back to non-encrypted won't reset the partition, which will remain a 12 GB brick of unusable space; at least, until you format it back to vfat, either through Odin or through a compatible mkfs.vfat.

Here are lines which caught my interest. This is from an encrypted CM10.1 20120603, which has been cleanly restarted once (and doesn't see the mount point anymore).

--------- beginning of /dev/log/main
I/installd( 1845): installd firing up
E/cutils ( 1845): Failed to read /data/.layout_version: No such file or directory
D/installd( 1845): Upgrading /data/media for multi-user
D/installd( 1845): Upgrading to shared /data/media/obb
--------- beginning of /dev/log/system
I/Vold ( 1837): Vold 2.1 (the revenge) firing up
I/DEBUG ( 1839): debuggerd: Jun 3 2013 00:37:20
D/Vold ( 1837): Volume sdcard0 state changing -1 (Initializing) -> 0 (No-Media)
D/Vold ( 1837): Volume sdcard1 state changing -1 (Initializing) -> 0 (No-Media)
D/Vold ( 1837): Volume usbdisk0 state changing -1 (Initializing) -> 0 (No-Media)
I/Netd ( 1838): Netd 1.0 starting
D/Vold ( 1837): Volume sdcard0 state changing 0 (No-Media) -> 2 (Pending)
D/DirectVolume( 1837): DirectVolume::handlePartitionAdded -> MAJOR 179, MINOR 1, PARTN 1
W/InterfaceController( 1838): Error (Symbol not found: ) while searching for the interface command fini function
D/DirectVolume( 1837): DirectVolume::handlePartitionAdded -> MAJOR 179, MINOR 2, PARTN 2
D/DirectVolume( 1837): DirectVolume::handlePartitionAdded -> MAJOR 179, MINOR 3, PARTN 3
D/DirectVolume( 1837): DirectVolume::handlePartitionAdded -> MAJOR 179, MINOR 4, PARTN 4
D/DirectVolume( 1837): DirectVolume::handlePartitionAdded -> MAJOR 179, MINOR 5, PARTN 5
D/DirectVolume( 1837): DirectVolume::handlePartitionAdded -> MAJOR 179, MINOR 6, PARTN 6
D/DirectVolume( 1837): DirectVolume::handlePartitionAdded -> MAJOR 179, MINOR 7, PARTN 7
D/Vold ( 1837): Volume sdcard0 state changing 2 (Pending) -> 1 (Idle-Unmounted)
D/DirectVolume( 1837): DirectVolume::handlePartitionAdded -> MAJOR 259, MINOR 0, PARTN 8
E/DirectVolume( 1837): Partition '/devices/platform/dw_mmc/mmc_host/mmc0/mmc0:0001/block/mmcblk0/mmcblk0p8' has a different major than its disk!
W/Vold ( 1837): Duplicate state (1)
D/DirectVolume( 1837): DirectVolume::handlePartitionAdded -> MAJOR 259, MINOR 1, PARTN 9
E/DirectVolume( 1837): Partition '/devices/platform/dw_mmc/mmc_host/mmc0/mmc0:0001/block/mmcblk0/mmcblk0p9' has a different major than its disk!
W/Vold ( 1837): Duplicate state (1)
D/DirectVolume( 1837): DirectVolume::handlePartitionAdded -> MAJOR 259, MINOR 2, PARTN 10
E/DirectVolume( 1837): Partition '/devices/platform/dw_mmc/mmc_host/mmc0/mmc0:0001/block/mmcblk0/mmcblk0p10' has a different major than its disk!
W/Vold ( 1837): Duplicate state (1)
D/DirectVolume( 1837): DirectVolume::handlePartitionAdded -> MAJOR 259, MINOR 3, PARTN 11
E/DirectVolume( 1837): Partition '/devices/platform/dw_mmc/mmc_host/mmc0/mmc0:0001/block/mmcblk0/mmcblk0p11' has a different major than its disk!
W/Vold ( 1837): Duplicate state (1)
D/DirectVolume( 1837): DirectVolume::handlePartitionAdded -> MAJOR 259, MINOR 4, PARTN 12
E/DirectVolume( 1837): Partition '/devices/platform/dw_mmc/mmc_host/mmc0/mmc0:0001/block/mmcblk0/mmcblk0p12' has a different major than its disk!
W/Vold ( 1837): Duplicate state (1)
W/Vold ( 1837): Duplicate state (1)
W/Vold ( 1837): Duplicate state (1)
W/Vold ( 1837): Duplicate state (1)
W/Vold ( 1837): Duplicate state (1)
I/cm ( 1875): ____ _ _ ____ _ _ ____ ____ ____ _ _ _ _ ____ ___
I/cm ( 1910): | \_/ |__| |\ | | | | __ |___ |\ | |\/| | | | \
I/cm ( 1915): |___ | | | | \| |__| |__] |___ | \| | | |__| |__/

[...]

I/SystemServer( 2183): Mount Service
D/MountService( 2183): got storage path: /storage/sdcard0 description: Internal storage primary: true removable: false emulated: false mtpReserve: 0 allowMassStorage: true maxFileSize: 0
D/MountService( 2183): addVolumeLocked() StorageVolume [mStorageId=0 mPath=/storage/sdcard0 mDescriptionId=17040710 mPrimary=true mRemovable=false mEmulated=false mMtpReserveSpace=0 mAllowMassStorage=true mMaxFileSize=0 mOwner=null]
D/MountService( 2183): got storage path: /storage/sdcard1 description: SD card primary: false removable: false emulated: false mtpReserve: 0 allowMassStorage: true maxFileSize: 0
D/MountService( 2183): addVolumeLocked() StorageVolume [mStorageId=0 mPath=/storage/sdcard1 mDescriptionId=17040711 mPrimary=false mRemovable=false mEmulated=false mMtpReserveSpace=0 mAllowMassStorage=true mMaxFileSize=0 mOwner=null]
D/MountService( 2183): got storage path: /storage/usbdisk0 description: USB storage primary: false removable: true emulated: false mtpReserve: 0 allowMassStorage: false maxFileSize: 0
D/MountService( 2183): addVolumeLocked() StorageVolume [mStorageId=0 mPath=/storage/usbdisk0 mDescriptionId=17040712 mPrimary=false mRemovable=true mEmulated=false mMtpReserveSpace=0 mAllowMassStorage=false mMaxFileSize=0 mOwner=null]

[...]

D/DirectVolume( 1837): Checking for bad partition major number
D/DirectVolume( 1837): Found bad partition
E/DirectVolume( 1837): Fixing major number from 179 to 259 for partition 11
D/DirectVolume( 1837): Checking for bad partition major number
D/DirectVolume( 1837): Found bad partition
E/DirectVolume( 1837): Fixing major number from 254 to 259 for partition 10
I/Vold ( 1837): /dev/block/vold/259:10 being considered for volume sdcard0
D/Vold ( 1837): Volume sdcard0 state changing 1 (Idle-Unmounted) -> 3 (Checking)
D/Vold ( 1837): Trying to get filesystem type for /dev/block/vold/259:10
E/Vold ( 1837): None or unknown filesystem on /dev/block/vold/259:10
D/Vold ( 1837): Volume sdcard0 state changing 3 (Checking) -> 1 (Idle-Unmounted)
D/MountService( 2852): volume state changed for /storage/sdcard0 (unmounted -> checking)
D/MountService( 2852): sendStorageIntent Intent { act=android.intent.action.MEDIA_CHECKING dat=file:///storage/sdcard0 (has extras) } to UserHandle{-1}
D/MountService( 2852): volume state changed for /storage/sdcard0 (checking -> nofs)
D/MountService( 2852): sendStorageIntent Intent { act=android.intent.action.MEDIA_NOFS dat=file:///storage/sdcard0 (has extras) } to UserHandle{-1}
E/MountService( 2852): Boot-time mount failed (-3)