[Desire Android Development] melethron:
OP updated. Here is the new log of the first and second boot.

I colored the unaligned values red and the aligned ones green.

===========================================================
data2whatever log
===========================================================

=============================
Mon Dec 27 20:05:31 UTC 2010
=============================

+++ Your Partition(s) are NOT aligned and data2whatever modified them:
----------------------------------------------------------------------

+++ Your SD-Ext Partition started at sector: 27117720
=> your SD-ext partition was NOT 1024k aligned
and it should start at following sector: 27119616

+++ Your Swap Partition started at sector: 30105810
=> your Swap partition was NOT 1024k aligned
and it should start at following sector: 30107648

+++ OLD Partition table of your SD-Card:
----------------------------------------

__________________________fdisk_Partition_table_____________________________

Disk /dev/block/mmcblk0: 15.9 GB, 15931539456 bytes
255 heads, 63 sectors/track, 1936 cylinders, total 31116288 sectors
Units = sectors of 1 * 512 = 512 bytes

Device Boot Start End Blocks Id System
/dev/block/mmcblk0p1 63 27117719 13558828+ c Win95 FAT32 (LBA)
/dev/block/mmcblk0p2 [COLOR="Red"] 27117720[/COLOR] [COLOR="Red"] 30105809[/COLOR] 1494045 83 Linux
/dev/block/mmcblk0p3 [COLOR="Red"] 30105810[/COLOR] 31101839 498015 83 Linux
____________________________________________________________________________

+++ The Partitiontable has been modified
----------------------------------------

__________________________fdisk_Partition_table_____________________________

Disk /dev/block/mmcblk0: 15.9 GB, 15931539456 bytes
255 heads, 63 sectors/track, 1936 cylinders, total 31116288 sectors
Units = sectors of 1 * 512 = 512 bytes

Device Boot Start End Blocks Id System
/dev/block/mmcblk0p1 63 27117719 13558828+ c Win95 FAT32 (LBA)
/dev/block/mmcblk0p2 [COLOR="YellowGreen"]27119616[/COLOR] [COLOR="YellowGreen"]30107647[/COLOR] 1494016 83 Linux
/dev/block/mmcblk0p3 [COLOR="YellowGreen"]30107648[/COLOR] 31116287 504320 83 Linux
____________________________________________________________________________

+++ The SD-ext partition got formated with EXT4 afterwards:
-----------------------------------------------------------

____________________________mkfs.ext4_output________________________________
Filesystem label=userdata
OS type: Linux
Block size=4096 (log=2)
Fragment size=4096 (log=2)
Stride=0 blocks, Stripe width=0 blocks
93504 inodes, 373504 blocks
0 blocks (0.00%) reserved for the super user
First data block=0
Maximum filesystem blocks=385875968
12 block groups
32768 blocks per group, 32768 fragments per group
7792 inodes per group
Superblock backups stored on blocks:
32768, 98304, 163840, 229376, 294912

Writing inode tables: 0/12 1/12 2/12 3/12 4/12 5/12 6/12 7/12 8/12 9/1210/1211/12done
Creating journal (8192 blocks): done
Writing superblocks and filesystem accounting information: done

This filesystem will be automatically checked every 31 mounts or
180 days, whichever comes first. Use tune2fs -c or -i to override.
____________________________________________________________________________

+++ Filesystem check found no errors - no log attached
-------------------------------------------------------

###################################################################

=============================
Mon Dec 27 20:11:59 UTC 2010
=============================

+++ Your Partition(s) are already aligned and data2whatever didn't modify them
-------------------------------------------------------------------------------

+++ Filesystem check found no errors - no log attached
-------------------------------------------------------

###################################################################

I also made a test before that (log looks slightly different) with only swap partition not aligned (it will still erase sd-ext then because of the end sector.

-----------------------------
Mon Dec 27 19:18:19 UTC 2010
-----------------------------

+++ Your Partition(s) are NOT aligned and data2whatever modified them:

+++ Your Swap Partition started at sector: 30117188
=> your Swap partition was NOT 1024k aligned
and it should start at following sector: 30117888

+++ OLD Partition table of your SD-Card:

Disk /dev/block/mmcblk0: 15.9 GB, 15931539456 bytes
255 heads, 63 sectors/track, 1936 cylinders, total 31116288 sectors
Units = sectors of 1 * 512 = 512 bytes

Device Boot Start End Blocks Id System
/dev/block/mmcblk0p1 63 27117719 13558828+ c Win95 FAT32 (LBA)
/dev/block/mmcblk0p2 [COLOR="YellowGreen"]27119616[/COLOR] [COLOR="Red"] 30105809[/COLOR] 1493097 83 Linux
/dev/block/mmcblk0p3 [COLOR="Red"] 30117188[/COLOR] 31116287 499550 82 Linux swap

+++ The Partitiontable has been modified
--- This is the NEW Partition table of your SD-Card:

Disk /dev/block/mmcblk0: 15.9 GB, 15931539456 bytes
255 heads, 63 sectors/track, 1936 cylinders, total 31116288 sectors
Units = sectors of 1 * 512 = 512 bytes

Device Boot Start End Blocks Id System
/dev/block/mmcblk0p1 63 27117719 13558828+ c Win95 FAT32 (LBA)
/dev/block/mmcblk0p2 [COLOR="YellowGreen"]27119616 [/COLOR] [COLOR="YellowGreen"]30117887[/COLOR] 1499136 83 Linux
/dev/block/mmcblk0p3 [COLOR="YellowGreen"] 30117888[/COLOR] 31116287 499200 83 Linux

+++ The SD-ext partition got formated with EXT4 afterwards:

Filesystem label=userdata
OS type: Linux
Block size=4096 (log=2)
Fragment size=4096 (log=2)
Stride=0 blocks, Stripe width=0 blocks
93696 inodes, 374784 blocks
0 blocks (0.00%) reserved for the super user
First data block=0
Maximum filesystem blocks=385875968
12 block groups
32768 blocks per group, 32768 fragments per group
7808 inodes per group
Superblock backups stored on blocks:
32768, 98304, 163840, 229376, 294912

Writing inode tables: 0/12 1/12 2/12 3/12 4/12 5/12 6/12 7/12 8/12 9/1210/1211/12done
Creating journal (8192 blocks): done
Writing superblocks and filesystem accounting information: done

This filesystem will be automatically checked every 31 mounts or
180 days, whichever comes first. Use tune2fs -c or -i to override.

+++ Filesystem check found no errors - no log attached

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