Arduino Due Real Time 3x slower

Hi, I'm trying to implement a Real Time Transfer Function in Arduino DUE, happens that it appears to be 3x slower than real time. My TF has a 1 second TAU and I used all the range for Sample Time, from 10ms to 1us, being this time my timer interruption period, the interruption routine is where I update the TF. I measure the interrupt in an oscilloscope and the period it's ok, and I made sure that everything within the routine was being executed, but my TF Tau is about 3 seconds in every test.

The worst part is that when I was supper tired and I decided to give up, I implemented the same routine in Arduino UNO with and external DAC - MCP4725, and it worked.

Anyone with the same problem?? I still want to use Arduino DUE in this project of mine mainly because of native DACs, once the MCP limits me in time (linked to I2C).

Without your program, scheme and detailed description of what you are trying to do, probably no one will 'guess' what your problem is.

The problem is not in the code, and demands someone who is working with the same subject.