Once I open FPGA reference, my project slows down until I close it

I have been struggling with the combination of FPGA and processor. Because if I open the FPGA reference, there is no problem at all. Also, if I use digital inputs as simple as a button, it doest'n affect either. But, once I open ANY FPGA reference, and y have any active Digital Output / Input or Analog... It becomes the slowest loop on earth. Reaching almost 170 ms per iteration. In the image I have a complete void FPGA vi. What can I do to solve this?