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Mpu6050 Arduino DUE connection problems

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Hi guys,

I come here, to ask you all nice people one tricky question.But for the beginning  I will describe you my project which I am working on.

My project is quadcopter, but not normal one, on board should be raspberry pi and arduino due with mpu6050. Basically everything works very well but not always. Here comes the problem. Sometimes Arduino DUE cant connect to mpu6050 over I2C. Sometimes it can and after restart of arduino DUE it again cant connect. Afterwards I have to power off arduino DUE and than power it again on. Than it works. So it looks to me some problem with registers or probably as I read, it can be with pull-ups on I2C. I was trying to repair it for a month but I could not, after lot of time I am trying to contact some person or group of people who could help me. I would be happy for all kinds of help. 

Here  I am posting also my code on github and some pics of quadcopter.

Little description of my project. On pc runs ground control written in C# which generates control strings and than sends them over network connection through sockets to raspberry pi, it executes them and then when necessary sends directly over serial to arduino DUE.
Arduino DUE takes care for PIDs and sensors staff. 


When I use example dmp from i2cdevlib it happens the same.One I can next time I can not connect. 

Please I will be happy for all kind of help!

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