On the quadrature encoder issue, I can tell you that I also had similar problems in a prototype project with the StarterKit with this component working with a mechanical encoder (with RC filtered outputs). I got some improvement by adding two inverters into the TopDesign. I had also to play with some different clock frequencies to get the best results. Not perfect, but much better.
Can you let us know what is the Bus Clock frequency you are using?
In the latest version of PSoC Creator(PSoC Creator 1.0), there is a Sync Component. This can be used to synchronize the external signal with the system Clock. This will help eliminate the missing of counts.