Coming from Europe...
KLM flies a very similar route on their Amsterdam to Kuala Lumpur.
http://flightaware.com/live/flight/KLM809/history/20140716/1850Z/EHAM/WMKK
The flight originated from Amsterdam. Every day MH-17 flies the same route to KL from Amsterdam.
These onboard maps are never 100% accurate anyway. Also, due to other air traffic, turbulence, headwinds, etc, the route can easily be 20-50 KM from the intended path, as directed by air traffic controllers.
I’m a window seat guy, and fly Delta from Atlanta - Seattle- Atlanta multiple times a year, and we never follow the same exact path. For example, last month we flew directly over Omaha, Nebraska, but the return had us at least 100 miles south of there.
The Amsterdam route goes right over Sevastopol, and there was a warning to avoid flying over occupied Crimea, and especially Russian military base in Sevastopol.
It looks like an evasive action. See Kristinn's map at 91 for another airline.