Colleen,
Like others, I am somewhat confused by the wording of this observation ...
Clearly, the auditor cannot be takling about "measuring equipment" since you are using a software tool instead of a voltmeter or a micrometer. However, what about the last paragraph of clause 7.6 (ISO 9001:2000) where it says "... the ability of computer software to satisfy the intended application shall be confirmed ... prior to use ..." It also refers to ISO 10012:2003 (that is the current version of what it actually says!) for guidance. 10012 has some requirements at 6.2.2: "Software ... shall be documented, identified and controlled ... tested and/or verified prior to initial use, approved and archived. Testing shall be to the extent necessary to ensure valid measurement results."
This seems to be saying that the commercial testing software that you use for testing your developed code must be validated somehow. Also, it must be placed under version control and re-tested any time it is patched or upgraded. As a guess, I think you would have to develop a test module that is verified by some other means, and contains examples that the test software should catch as good, questionable or bad (or whatever it does.) Then this test module becomes your "calibration standard" and is used to verify the testing software.
In my opinion, the intent should be that -- with respect to the commercial testing software you are using -- you can verify that the version in use operates as intended with samples of "known good" and "known bad" code from your development process. Both the test software and the code samples have to be documented and controlled.
I may have more suggestions tomorrow ... my copy of ISO 9000-3 (Guide to applying 9001:1994 to software development) is gathering dust at home since I don't do that in this job. By the way, that document is near the end of a revision, and may be released by the end of the year as ISO/IEC 90003.