I had to make a small addition to the Quick Start Guide doc and pdf files today. I discovered while helping a customer that I never quite said to click the ‘Use All’ button on the advection form! (At least I can’t find any mention of it where I should have made the point). This could certainly have caused confusion, at least when using the program manually.
Basically, I added a couple of paragraphs and one extra sentence to another paragraph. The screen shots are still slightly outdated (from WXSIM 11.8 and WXSIMATE 3.7), but close enough.
Hope that helps! 
Tom