Accessing magnetometer results in MPU-9250
In case you still need the help, Have you tried reading the ST2 register every time also? There is a sentence in section 8.3.5. of the data sheet "Therefore, when any of measurement data is read, be sure to read
ST2 register at the end." 
I also had problems with the continuous modes, so I switched to triggered mode.

The two things solved my data problems with this chip.

Best of luck.
Tom