I played with the MPU6050 as an inertial guidance system a few years back. I used an Arduino Nano and cursed the day I started the project because the darned thing froze, which is not the problem you are having. Still, because Invensense makes it hard to work with its chips, the MPU6050_6Axis_MotionApps20.h was “sniffed” from somewhere so it is setup for some device other than an Arduino. In MY case it turned out to be the FIFO rate. I found that the Arduino couldn’t handle a rate above 100 Hz. The default for this one is 200Hz. I can’t remember why I decided to look at that parameter… instinct, dumb luck… but I got it to work like a champ.
I don’t really understand using it as a joystick game controller and a parameters in that program could very well be the issue. However, you might be lucky and just need to duplicate my fix.
In the code from the website this appears to happen in lines 321 and 322. Anyway, that’s just a suggestion and just requires a simple code change.