I am having the same problem with a newly purchased ASUS U46e-bal6 which
has a WD7500BPKT-80PK4T0 (750GB drive).  I have installed ubuntu several
times both manually configuring partitions and letting ubuntu create
them, all with the same result.  Disk utility tells me that my extended
partition is misaligned by 1024 bytes

****************************************************************************************

sudo parted -l
Model: ATA WDC WD7500BPKT-8 (scsi)
Disk /dev/sda: 750GB
Sector size (logical/physical): 512B/4096B
Partition Table: msdos

Number  Start   End    Size    Type      File system     Flags
 1      1049kB  726GB  726GB   primary   ext4            boot
 2      726GB   750GB  24.3GB  extended
 5      726GB   750GB  24.3GB  logical   linux-swap(v1)


***************************************************************************************




** Attachment added: "screenshot of disk utility"
   
https://bugs.launchpad.net/ubuntu/+source/ubiquity/+bug/879387/+attachment/2646083/+files/Screenshot%20at%202011-12-24%2016%3A22%3A22.png

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https://bugs.launchpad.net/bugs/879387

Title:
  Partitions misaligned on advanced format drive WD20EARX

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