FAI disk partitioning

[RU Admin]

Does anyone know how to fix this error without wiping out all of the 
partitions on the drive:
    ERROR: unable to preserve partition /dev/sda2. Partition is not DOS
    aligned. at /usr/sbin/setup_harddisks line 475, <FILE> line 7.
I've tried everything but it doesn't seem like anyone knows how to fix 
this "alignment" issue...

Anyone know if I can comment out that check in the setup_harddisks?  Will 
that work, or will the machine probably not boot afterwards?

Thanks for any help!