Usually what I do is reduce the size of the partition on the disk I want to use by 10 or 15 GB. Then use the Linux distro's formatting procedure to use the "free space" and allow it to make the 2 or 3 Linux paritions it wants to make. That way I don't muck with the NTFS partition and never have any trouble. Still got Xandros 2.0 lurking on my harddrive as a dual boot possiblity. Still wish to use it more, but there is just tooooo much exciting Windows software out there!
difficult to imagine the new noise has anything to do with reformatting.