Questions and postings pertaining to the development of ImageMagick, feature enhancements, and ImageMagick internals. ImageMagick source code and algorithms are discussed here. Usage questions which are too arcane for the normal user list should also be posted here.
PSD images have some operators that ImageMagick does yet support and that could be the cause of the problem. The best path forward would be to post URL's to one or two problematic images so we can try it here and trace the source of the problem.
I got pretty good results converting your PSD with the -flatten option with ImageMagick 6.0.1-2. However it's not perfect. We will shoot for a patch to the PSD image reader for the next minor release. Thanks for the problem report.