Hi Spencer!
The device I am using is a PCI6024-E board. I have contacted the NI Suport and now I see what I was doing wrong: in fact, I was calling a DIO Port Config.vi for each of the ports ("Port Read" and "Port "Write"), but it was done inside of a While loop (usually, most of the applications here in the lab are recursive, so it´s common for us to use big while loops for the whole program). Putting them outside (as you said, at the beginning of the program), it worked! Actually, I can´t see any reason for the program to work when the calling is outside the loop, but the important is that now it´s running properly.
Thanks a lot, Spencer!