I'm guessing that Justflight buys them in bulk at a substantially cheaper rate than what we pay for a single copy, and then when sales slow down or need a boost, they can afford to knock a bit off the MSRP and make it look like a great deal.
Whereas the Wilco site one is more aimed at the newbie payware buyer who doesn't know they can get it cheaper at places like justflight or the pilotshop and such.