I think the dish is good but your pointing is bad. You are making bad assumption based on the info from the Align-a-Site. It's a good tool but it's only a tool. I would get the skew set properly, verify that the stand it plumb and level, set the proper elevation and start anew. With that done you should be able to pull up the signal meter screen for 101 transponder 1 and peak the signal. You could even do this with the skew set to 0 if you like and verify a good signal. Now, if you are not getting 70+ on the majority of transponders on 99 or 103 you need to very slightly adjust the skew in the recommended direction (or the other if that's not working) until you get good numbers. This might mean that you also need to adjust the az. and el. slightly as the dish is moved in skew (tilt). When you move the skew way out from the recommendation you have do chance of receiving all 3 satellites.
