Andreas, perhaps you'd try out the attached patch which attempts to resolve your problems with my stripping out of the hard coded additions to the PATH environment variable for MacOSX, replacing it with a LyXRC::path_prefix variable.
This attempt runs <system support>/configure after the various lyxrc files have been read. The patch should apply to a clean CVS head. You'll still need to set path_prefix manually, just as you've done previously. Regards, Angus
prepend_path_14x.diff.bz2
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