All I am saying is that "if" there is a problem with the PayPal payment module processing orders with promotions, you can investigate it since you have the source to debug it. I assume that since you are using KonaKart, you or someone in your team knows their way around a java program.
We will also take a look, but cannot guarantee any response times since you aren't under a support agreement. If we find a problem and fix it, we'll probably make the fix available in the next release.