You can do lots of things with developers that are not recommended by the manufacturer, and X-Tol at 1:3 is not far fetched at all. So I don't think that is the problem. My first thought, assuming that your exposures really are good, is that you just need to do the trials to figure out the right time to use at 1:3. You have just done trial number one. If you estimate that they are 30 percent overdeveloped, then you know what to try next time: less time. That will get you closer, and the next time closer still, and so on.
It's also possible that you just shot in very contrasty light, or that you are not judging the negatives properly when you say that they are exposed properly. If the whole neg is too thick, then the shots are overexposed. Remember that the darkest areas in the print should look almost clear on the neg. If you shot in pretty standard contrast light, and there is nothing on the neg that is truly clear or close to it, then they are probably overexposed.
Is it possible to take a picture of the negs against a window, or better yet, a light box, and post it here?