This issue can arise if BootIt NG 1.26d or lower was used to perform the partition operation(s) and happens because the BOOTSECT.DOS (or any other) file is not updated to reflect the new partition size/type/location.
To solve this issue, enable/use the Multi-OS feature instead of the WinNT/2K/XP boot manager or use a hex editor to update the BOOTSECT.DOS file. If you enable Multi-OS and are only dual-booting one WinNT/2K/XP - DOS/Win9x/Me combination, then you can remove all but one of the files (such as config.sys or boot.ini) in the multi-os group to speed up boot time.
Starting with version 1.26e, the BOOTSECT.DOS file will be updated. Other files which you may have (manually) captured and (manually) setup to work with the ntldr will not be updated.