I'd say your company got gypped if they spent $400k on such a fragile piece of software. What company produced this software, so the rest of us can steer clear of their incompetence?
If it was written to work with IE6 (as was a lot of software in the day) it was likely written in the era when IE6 was THE target market. Simply put, IE6 was the only game in town, really. If you wanted to make dynamic applications that were worth a damn, you wrote it for IE6.
That said, I agree that in this day and age, it is inexcusable.
One other point, you may be unaware (as I was until pointed out to me) that 'gypped' is a racial slur against Romani (or broader, Italians).
It was not my company and I had nothing to do with the purchase of the software. Also, if that $400k piece of software is unique and gives the company a tremendous competitive advantage, who cares if it's only compatible with Lynx? Not every app has to work everywhere. It has to be stable within its own system requirements.