I'll hazard a guess you're using the Acronis POS that is labeled for each drive manufacturer. It didn't work for me.
If it's a partition with data, you'll need something like the Paragon Alignment Tool (no longer free, but does work). Alternatively, copy the partition to somewhere else and use an alignment-aware tool to copy it back.
If it's an empty partition and you're using XP, you need either an alignment-aware partitioning tool (I don't know of any free ones, unfortunately) or the MS DISKPAR utility (not DISKPART).
It's probably easier just to create the partition on a Windows 7 box, even if you then move it to an XP box.