We created this plugin for use by publishers of scientific journals. They had a similar problem that MathML could not be faithfully rendered by the 3B2 MathML library. Our solution was to use MathFlow Equation Composer to render the equations dynamically. This works through the use of the EquationComposer.dll, to which we pass MathML markup during formatting. We then load the Equation Composer EPS or GIF into APP and display that on the page. We cache all images for speed, and the DLL integration is seamless.
This is not available as a standalone product, but we could implement this solution for your APP template if required. The tool is "GMA" (GPSL MathML for APP) and you can find out more by contacting info@gpsl.co (www.gpsl.co).