I think @RickardU hit the nail on the head. The problem is probably with the perception of your role due to your title. An auditor is generally seen as someone who's job it is to check other peoples work and find their deficiencies and failures. That role is often seen as an adversarial position rather than as a member of the team that adds value to the product.
I would have a talk with your manager/Director/CIO or whomever it is that you report up to and is responsible for your activities being a success. I would try convince them to re-brand your role as IT Security Champion. Take the focus off of the audits and those things seen as adversarial, and focus on integrating your role as an asset in the project design and development process.
In your role as Champion your goals should be to get the team to focus on including you in the early planning and discussions of projects to integrate the security component into the design. Get the teams involved in discussions on how to improve and get their engagement in the process of improving the IT Security at your company.
One part of your role will still be the audits. But those should be done discreetly, and reports should be submitted to management, not to the teams. Focus on trends and persistent issues, rather than individual incidents, unless those incidents actually result in a breach. It is the managers job to handle the incidents, it is your function to make them aware of the the problems that keep popping up, or are inherent in the design.
When you get assigned to lead the charge in solving an issue, involve the teams in finding the solution. Get them to help solve the problem rather than providing a solution for them to implement. This will have a two fold benefit of, getting them engaged in the security process, and getting them to think about these problems proactively going forward.