Pathway puts in glottals and hyphens as alphabetic dividers in the dictionary. It seems it has to do with what I have in the citation form. When the citation form of an entry begins with a hyphen or glottal it puts in an alphabetic divider. Is this expected behaviour? See the attached extract.
I am fairly certain the letter headers are generated by the XHTML export in Flex before the Pathway program gets to look at it. You can try using the XHTML export and look at the results with Firefox to see if the letter headers have been inserted. I think the ignored character syntax is giving you trouble. I changed the sort specification (Format, Writing Systems, Modify — Akoose, Sort) to:
&ɛ << ʼɛ
& ɛ < ə <<< Ə
&ə << ʼə
& a << aa << á << áá << â << áa << ǎ << aá << ʼa << ʼaa << ʼá << ʼáá << ʼâ << ʼáa << ʼǎ << ʼaá
&ɔ << ʼɔ
& s << ʼs
& [last tertiary ignorable] = \( = \)
And with that specification, I didn’t have the problem.