I've also been having this strange problem ever since I started using P3D V2. Scenarios was completely broken, flights were starting in the middle of nowhere, and P3D crashes on startup when selecting to have the Scenario Startup Screen show on startup.
I've finally found a fix. The trick was changing the system locale: Control Panel -> Region and Language -> Administrative -> Change System Locale
I live in Hong Kong, and with the system locale set to Hong Kong, China by default, the P3D situation files inside My Documents were showing random Chinese characters when I opened them using notepad. Ever since changing the locale to an English speaking location, the files no longer show weird Chinese characters in notepad.
Everything now works correctly. No more crashes and unexpected behavior when loading scenarios, and flights start correctly with the selected scenario.