Harold,
I think the problem breaks down to several points, but most of them can be tied to inexperience. A lot of posters who complain about the Atlas turnouts are new modellers. To my curmudgeonly mind, that means that a) their track-laying skills are suspect and b) they don't know where to look for what's causing the problems.
The main points I see for problems with Atlas turnouts:
2) tracklaying skills. There may be dips, bumps or twists to the turnout that cause it to create problems, that the inexperienced eye can't catch. Turnouts don't like being bent in the middle... they like a nice flat surface to lay on. Also, a lot of problems with the Atlas turnouts can be solved by chamfering the points so that the tip of the point rail is not square, which eases wheels up onto the point.
3) equipment. Kinda the yin to #1's yang, and again, sometimes related to experience. Out of gauge wheels or toy trainset rolling stock with huge flanges don't like the Atlas frogs. Long wheelbase locos (steam and diesel) really aren't happy on 15-18" curves, Snap and #4 turnouts.
3) equipment. On a different note, newer, better rolling stock with RP25 flanges and shallower wheel treads sometimes don't like those Atlas Code 100 frogs.
4) the turnout. This is usually the last case, but sometimes the turnouts themselves are bad. The rivets that hold the points may be loose or tight, the point rails may be loose or bent at the throwbar, and so not close properly with the stock rail, or may protrude above the stock rail. There may be some flash in a flangeway or the frog, or the rails may not be seated properly at the frog.
Personally, I'm not a big fan of the Atlas code 100 turnouts, Custom Line or otherwise. I think the ties and "spikes" look big and clunky, and I'm not a fan of the rivets that hold the points (and why I'm also not a fan of Walthers/Shinohara). The Atlas code 83 turnouts look a little better, seem to run well (my LHS has them on their store layout, and they've been trouble-free for 4 years of steady use).