Perhaps you could roll back the Nvidia drivers to the version that worked well for you and just update Nvidia Inspector. Version 1.9.6.6 has the additional Vsnyc options as seen below. Great advice from the other posters!
There is an option for 1/2, 1/3, 1/4 in the drop down in the vsnyc option. Remember to select MS Flight Simulator 2004 under profiles. I use these settings for Nvidia Inspector in FS9 courtesy of NickN.