Haha. I've done very little interviewing/hiring, but if I was the interviewer I'd probably laugh along with you at that point - especially if I had just pressed you for more details about why you're leaving the current job.

Maybe it's how you're saying it, and not what you're saying? Is there somebody you could practice with? Somebody who could point out body language or tone of voice or other cues that could be giving interviewers the wrong impression about you?

One other possibility...

Maybe round out that story by mentioning how you (or the team you were a part of, even if you weren't the lead person on the effort) tried to solve that problem in a constructive way. "We gave our boss a presentation on three popular, low-cost issue trackers that we tried and liked... to no avail." Surely your next employer will make some decisions you don't agree with - they're wondering how you will handle them!