After some searching, it seems that the boot process on the iMX233 is fairly non-standard. By default it looks for a "Boot Control Block" (BCB) in the last block of the SD card.
Examining the original SD card, find the last block using fdisk -l:
Disk /dev/mmcblk0: 1996 MB, 1996488704 bytes
4 heads, 16 sectors/track, 60928 cylinders, total 3899392 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x0f6c2d46
Device Boot Start End Blocks Id System
/dev/mmcblk0p1 2048 32000 14976+ 53 OnTrack DM6 Aux3
/dev/mmcblk0p2 32001 200000 84000 83 Linux
/dev/mmcblk0p3 200001 400000 100000 83 Linux
/dev/mmcblk0p4 400001 3899391 1749695+ 83 Linux
There are 3899392 sectors.
Examine the last sector of the SD card using dd:
root@kali:~# dd if=/dev/mmcblk0 bs=512 count=1 skip=3899391 2> /dev/null | hexdump -C
00000000 33 22 11 00 01 00 00 00 04 00 00 00 04 00 00 00 |3"..............|
00000010 04 00 00 00 04 08 00 00 50 00 00 00 50 00 00 00 |........P...P...|
00000020 50 00 00 00 50 00 00 00 ef be ad de 00 00 00 00 |P...P...........|
00000030 01 00 00 00 02 00 00 00 03 00 00 00 04 00 00 00 |................|
00000040 05 00 00 00 06 00 00 00 07 00 00 00 08 00 00 00 |................|
00000050 09 00 00 00 0d 0a 00 00 00 0b 00 00 00 0c 00 00 |................|
00000060 00 0d 00 00 00 0e 00 00 00 0f 00 00 00 10 00 00 |................|
00000070 00 11 00 00 00 12 00 00 00 13 00 00 00 14 00 00 |................|
00000080 00 15 00 00 00 16 00 00 00 17 00 00 00 18 00 00 |................|
00000090 00 19 00 00 00 1a 00 00 00 1b 00 00 00 1c 00 00 |................|
000000a0 00 1d 00 00 00 1e 00 00 00 1f 00 00 00 20 00 00 |............. ..|
000000b0 00 21 00 00 00 22 00 00 00 23 00 00 00 24 00 00 |.!..."...#...$..|
000000c0 00 25 00 00 00 26 00 00 00 27 00 00 00 28 00 00 |.%...&...'...(..|
000000d0 00 29 00 00 00 2a 00 00 00 2b 00 00 00 2c 00 00 |.)...*...+...,..|
000000e0 00 2d 00 00 00 2e 00 00 00 2f 00 00 00 30 00 00 |.-......./...0..|
000000f0 00 31 00 00 00 32 00 00 00 33 00 00 00 34 00 00 |.1...2...3...4..|
00000100 00 35 00 00 00 36 00 00 00 37 00 00 00 38 00 00 |.5...6...7...8..|
00000110 00 39 00 00 00 3a 00 00 00 3b 00 00 00 3c 00 00 |.9...:...;...<..|
00000120 00 3d 00 00 00 3e 00 00 00 3f 00 00 00 40 00 00 |.=...>...?...@..|
00000130 00 41 00 00 00 42 00 00 00 43 00 00 00 44 00 00 |.A...B...C...D..|
00000140 00 45 00 00 00 46 00 00 00 47 00 00 00 48 00 00 |.E...F...G...H..|
00000150 00 49 00 00 00 4a 00 00 00 4b 00 00 00 4c 00 00 |.I...J...K...L..|
00000160 00 4d 00 00 00 4e 00 00 00 4f 00 00 00 50 00 00 |.M...N...O...P..|
00000170 00 51 00 00 00 52 00 00 00 53 00 00 00 54 00 00 |.Q...R...S...T..|
00000180 00 55 00 00 00 56 00 00 00 57 00 00 00 58 00 00 |.U...V...W...X..|
00000190 00 59 00 00 00 5a 00 00 00 5b 00 00 00 5c 00 00 |.Y...Z...[...\..|
000001a0 00 5d 00 00 00 5e 00 00 00 5f 00 00 00 60 00 00 |.]...^..._...`..|
000001b0 00 61 00 00 00 62 00 00 00 63 00 00 00 64 00 00 |.a...b...c...d..|
000001c0 00 65 00 00 00 66 00 00 00 67 00 00 00 68 00 00 |.e...f...g...h..|
000001d0 00 69 00 00 00 6a 00 00 00 6b 00 00 00 6c 00 00 |.i...j...k...l..|
000001e0 00 6d 00 00 00 6e 00 00 00 6f 00 00 00 70 00 00 |.m...n...o...p..|
000001f0 00 71 00 00 00 72 00 00 00 73 00 00 00 74 00 00 |.q...r...s...t..|
00000200
The magic number of 0x33221100 is mentioned in some Freescale documentation, though I was expecting to see it with the opposite endianness.
So to make a successful clone, choose a SD card of larger capacity to ensure nothing is overwritten (or you can resize partitions).
Take an image of the original card:
root@kali:~# dd if=/dev/mmcblk0 of=wholeSD.img
3899392+0 records in
3899392+0 records out
1996488704 bytes (2.0 GB) copied, 98.3687 s, 20.3 MB/s
Then take an image of just the last sector for the BCB:
root@kali:~# dd if=/dev/mmcblk0 bs=512 count=1 skip=3899391 of=BCB.img
1+0 records in
1+0 records out
512 bytes (512 B) copied, 0.000220203 s, 2.3 MB/s
Find out how big the new SD card is:
Disk /dev/mmcblk0: 2002 MB, 2002780160 bytes
4 heads, 16 sectors/track, 61120 cylinders, total 3911680 sectors
Units = sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disk identifier: 0x0f6c2d46
Device Boot Start End Blocks Id System
/dev/mmcblk0p1 2048 32000 14976+ 53 OnTrack DM6 Aux3
/dev/mmcblk0p2 32001 200000 84000 83 Linux
/dev/mmcblk0p3 200001 400000 100000 83 Linux
/dev/mmcblk0p4 400001 3899391 1749695+ 83 Linux
This one is larger with 3911680 sectors.
Move the whole card image onto the new card:
root@kali:~# dd if=wholeSD.img of=/dev/mmcblk0
13899392+0 records in
3899392+0 records out
1996488704 bytes (2.0 GB) copied, 1545.45 s, 1.3 MB/s
And then move the BCB image to the last sector of the card:
root@kali:~# dd if=BCB.img bs=512 count=1 seek=3911679 of=/dev/mmcblk0
1+0 records in
1+0 records out
512 bytes (512 B) copied, 8.4684e-05 s, 6.0 MB/s
Note the use of seek (output side) rather than skip (input side).
It is worth double checking that the last block has been written. Several cheap SD cards don't seem to work in the last sectors, possibly because they misreport size.
Now you have a booting card.