Here is the response from Jim Miller at Atlas below. I doubled/triple checked everything and I get the same result. Will likely ship my snap switches to Atlas, as that is the problem as far as I can see.
As a sidenote, does your program already have the diverging angles built into it, or is it measured and entered into the system? For some reason the diverging angle is the issue.
Jason,
I apologize again for the delay, but at long last we do have an answer to your question. Our chief mechanical design person assembled the track as described in the Atlas layout book #9 for HO-6. As you can see from the attached photograph, when assembled as described in Book #9, the track fits together the way it should.
I don’t know exactly what to tell you, but here are a few suggestions.
The track will not fit together properly unless you use EXACTLY the same quantity and size (length and/or curve radius) of Atlas–brand track sections and turnouts called for in the Atlas drawing of layout HO-6. I know that you said that you checked all of the track. However, since we got the track to do what the plan intended it to do here at Atlas, you will need to assemble your track in exactly the same way that we did, i. e., following the HO-6 plan. I recommend that you remove all of the track from your table, turn it upside down, and read what is written on the underside using a VERY BRIGHT light. If you cannot read what is stamped on the underside of a turnout or track section, you should replace it with the proper piece of new Atlas track.
Are you using any non-Atlas track? I ask this question because in one of your photos we spotted what appears to be an 18” radius curved terminal section that has the screws to which you connect power in the middle of the terminal section. Atlas has never made its curved terminal sections with the terminal screws in the center; I have no idea if non-Atlas track will work.
Atlas Snap Switches and Atlas Custom Line #4 turnouts look somewhat similar, but they are NOT interchangeable. You MUST use Atlas Snap Switches in layout HO-6.
The trackwork on the left side of layout HO-6 does NOT make a 180 degree turn. If you have the trackwork at the bottom of this layout parallel to the edge of the benchwork, the track at the top will be heading slightly inwards until you add the 1/3 18” radius sections specified in the plan.
Please don’t be discouraged. A number of our customers take a while to get their track the way they want it.
Jim Miller
Atlas Model Railroad Co., Inc. and Atlas O, LLC
378 Florence Ave.
Hillside, NJ 07205
USA
(908) 687-9590
jmiller@AtlasO.com