This is very common when welding frame rails, and is one of the reasons why some trucks only have three wheels in contact with the road. Try these.
1. document weld procedure very closely
2. repeat weld process exactly the same each time
3. as mentioned earlier try to alternate or balance welds to reduce the effect of thermal expansion as much as possible.
4. once you have a stable part/process and you can predict how much the part is moving during the weld process, now you can go back to your weld fixture and introduce a little "pre-bend" in the opposite direction so that your parts come out straight.
Been there, done that, got the scars
danno