5 minutes after I call them, I finally get a response to my email:
The "Section 508" and/or "W3C WCAG" accessibility standards have not changed and are static. These guidelines consist of elements which are objective (ex: presence of alt text or not), as well as subjective (ex: if you use color to convey information, ensure it contrasts sufficiently).
As you can appreciate, Watchfire as a proactive software company continues to make improvements to our accessibility scanning in effort to make more of the existing checking capability even better. The accessibility standards never change, but our checking methods are always improving. For example, quicker and more intelligent methods are now available in Bobby 5 which Bobby 4 did not have. Also, in later releases of our software we have been able to add more intelligence in our scanning abilities to include more of the "manual" user checks into our "automatic" checking to increase value in the product and remove less manual checking for the end user trying to ensure accessibility guideline conformance.
Therefore, when comparing new products to the older online Bobby scan (based on Bobby 4 engine), it is not uncommon to see differences in the reporting.
The free service at bobby.watchfire.com is based on an older technology and has some known issues that we have not yet been able to resolve. I think you will be more pleased with a newer service we have called WebXACT, http://webxact.watchfire.com/. This is based on a newer technology but it performs the same accessibility checks as the older service. WebXACT is also a more accurate sample of what the product now available for purchase is like. WebXACT, with some delay as new development is ongoing, will continue to be kept as up-to-date as possible to reflect our current scanning ability (including accessibility).
So basically, the response is, "Don't use Bobby, use WebXact, which is newer and better." OK, I can live with that. Except now I'm running into more accessibility problems.
They've diverged a bit from the W3C guidelines (Example: you fail if you have a LONGDESC without a "D-link" next to the image. I agree with Joe Clark when he says that D-Links are ugly and not terribly useful.)
My document also now fails because the frames aren't sized using percentages. That's the point of this document! The navigation frame should stay just large enough to show all the navigation content, and the rest of the window is devoted to the content area; if we allowed the frames to be fluid, the nav frame could be too small, or it could grow too large and steal screen real-estate from the content area.