Corruption in the files of the chkdsk utility itself is one possible cause of inconsistencies in test results. To obviate this, act to scan from a neutral environment whenever possible, such as through a DOS interface loaded from an outside optical disc.
Checking the file structure of your volume via different applications--such as from first-party and later with third-party software--can lead to inconsistent results if the programs are using different algorithms to determine error sections. To avoid this, always use the same application to perform your disk checking.
Other problems and corruption within the system can potentially contribute to inconsistencies. When in doubt, remove the drive from your system and plug it into a third-party machine (a friend or neighbor's computer) to repeat the check in a neutral environment.