what do the YELLOW connections mean on the simulation, I believe green is source, dark grey is sink and light grey is input is this correct ?.
edit
it would seem that if you change a high output to an input it turns yellow but why ? !!
Yellow means an input pin is high (for instance, it's an input and you have clicked it). If you single step through your program in simulation, you will see exactly which commands do what to each pin.