737NGX Loads Minimized in P3D V3.0

If while loading the PMDG 737NGX into P3D with the Estonia Migration Tool is installed.
The P3D screen minimizes and you can only see the loading bar and when loading is finished it shows a weird picture. The aircraft may also seem to not align with the ground (is over the ground, then under the ground and so on) and it looks like that each time the shaders are new generated. Sometimes the SIM crashes after finishing loading.
To correct:
Look up file MigrationTool.cfg in Migration Tool's install folder (usually C:\Program Files (x86)\Flightsim Estonia\Migration Tool). Open it woth Notepad, change line PMDG737=1 to PMDG737=0, save the file and start Prepar3D to see if this makes any difference.