Use native partitioning software whenever possible.
I can't comment further because there are far too few details. XP for example does not know about SATA drives and the boot manager for Vista and XP are frankly "a big mess of trouble."
I find that after trying to create a partition with Acronis Disk Director, I get the message "disk not found," after rebooting. I also tried using Paraagon Partitioning Manager. In this case after committing and rebooting there are simply no changes and no messages to the disk. I can get Vista Disk Manager to work probably because that doesn't require a reboot. Anyone know what could be causing these (boot related) third party software problems? I could add that lately I haven't been able to get Windows XP Installation to resume after rebooting either. It says, "operating system not found."