Well, I haven't got a clue on what I did to cause the problem, I was routing for ages, I had to swap two wires around on a chip, and when I recompiled and updated it all went very bad. Who knows what steps I performed in between.
Finally I recreated a new project, included my schematic and PCB file, and order was restored to the Universe. I just hope the problem doesn't came back.
Thanks for your help.
kv