Windows AIK 1.0 included a BOOTSECT.EXE tool that could update the boot sector to either a Windows Vista/Server 2008 (/nt60) or a Windows XP/Server 2003 (/nt52) version. But it didn't provide a way to update the master boot record (MBR). If you wanted to do that, you had to boot into the Windows recovery environment and then run "FIXBOOT /MBR". The downside of that: it can't easily be automated. (What's the difference between a boot sector and an MBR? Read up on it at http://www.microsoft.com/technet/prodtechnol/windows2000serv/reskit/prork/prcb_dis_qxql.mspx?mfr=true.)
The MBR code was updated for Windows Vista, and if you install Windows Vista using SETUP.EXE (e.g. straight from the DVD or using MDT Lite Touch) it will update the MBR appropriately. And running DISKPART "CLEAN" will also update the MBR. But if you aren't wiping the disk and aren't using SETUP.EXE, the old MBR would be left in place.
Why does this even matter? One noticeable reason: BitLocker wants to see a Windows Vista MBR, and won't let you enable BitLocker if it doesn't find one. So you need a way to do that, something easily automated. That something is a new version of BOOTSECT.EXE included in Windows AIK 1.1. This version has a new /MBR switch that takes care of installing the latest MBR.
This is actually related to why ConfigMgr 2007 SP1 requires Windows AIK 1.1: it wants to use the new BOOTSECT.EXE /MBR command, so it needs the latest BOOTSECT.EXE /MBR command. The old BOOTSECT.EXE will fail if you specify this previously-nonexistent command line option. (MDT 2008 Lite Touch uses slightly different logic: it tries the BOOTSECT.EXE /NT60 /MBR command and if it fails it tries again without the /MBR switch. So we can still support Windows AIK 1.0 and 1.1.)