Shortly after the release of GT6 update 1.17, our forums exploded in a flurry of posts as our users realized that something had changed in relation to the transmission tuning options in the game.
The related topic has generated hundreds of posts of testing and debate, and Polyphony Digital formally acknowledged the issue in a post on the official site. Specifically, they confirm that changes to only the Final Gear value in a “Fully Customizable Dog-Clutch Transmission” will be reset after leaving the Car Settings menu.
Polyphony reports they are working on the issue and will report when the issue is resolved in a future update. Until then, note that you can avoid the bug by modifying other gear values in addition to the Final Gear setting.