I don't think it's so much 'getting the molds right' that is the problem, I see it as simply failing to do the proper research, which is basically inexcusable considering the high investment costs of the tooling. Yes, sometimes compromises have to be made for molding something in plastic, but that's clearly not the issue here. Someone just wasn't doing their homework, and like Kyle said, it's most likely not the same person who's cranking out those beautiful Acelas and whatever else new that Spectrum is doing these days.
(Incidentally, Bachmann's F40PH has suffered the same fate as the Amfleets, even if it is part of the Spectrum line. The underbody detail is nicer this time, but the shell is still terribly inaccurate and makes one wonder what they really mean when they say 'completely retooled' each time they try to redo their older models.)
Like I said, my take on it is that since over the years people have accepted the Walthers model as the better one, Bachmann appears to have based their new versions on the Walthers shells, which is really not the way to go about it. The Walthers shells have been wrong ever since they were first introduced in the early 1980s, but because they were overall less toy-like and more model-like than the Bachmanns, they have been popularized as the way to go.
The fact is, they themselves seem to have been the result of improper research: comparing them to the
brass models imported previously by Soho, they feature the same incorrect cross-section, same oversized and misplaced vents, and the same shallow doorway detail. The only real difference is the windows, where Walthers made the center posts part of the glazing inserts. By contrast, as we've said, the original Bachmann shells were nearly spot-on, with none of the aforementioned errors. They're just a bit lacking in end and underbody detail, which is not too hard to fix.
So what it all boils down to is that Bachmann has someone who's not doing their job very well. Walthers, by contrast, has been putting out some amazing cars lately, and while I don't quite agree with all of their choices of prototype, the models are very accurate. Even the Amfleet II showed an attempt to correct some of the mistakes of their Amfleet I, but I imagine they didn't want to change everything so that the cars would still blend in well together. Now, if they were to finally try a remake of the Amfleet I - preferably without those annoying diaphragms - that would really be something to look forward to.