I am experiencing the same problem. My setup is 3.3V at 8MHz. Serial.print appears to be a contributing factor. I have been dumping the fifoCount variable and if it stays at 0 all is ok. Sometimes it starts higher and we get a "FIFO Overflow!" message and then it resumes ok. Other times the fifoCount grows and then nothing.
Both Arduino and MPU6050 are new to me. Have some MPU's with voltage regulators on order to try with a faster CPU.
I am wondering if the mpuInterrupt flag and while loop are at fault. If there are multiple messages available we should get them all so as to catche up the the device. Looks to me that we never eat more than packetSize element per interrupt.