The FDK 2.0 makeOTF can build a font identical to the makeOTF from 1.6. I suggest that use the ttx ( which is NOT the tx tool) tool from the FDK 2. to dump both fonts to XML and compare the two XML text files to see what's different. The XML version of the GSUB table is suitable only for programmers; to get a more useful text version of this to compare between the new and old version, use the command line:
spot -t GSUB=7
this will dump a feature-file syntax version, with notes about under which language and script the lookups are registered.
If you have made sure the PUA values are the same by applying them explicitly, the only other thing I can think of is that the FDK 2.0 makeotf does have different rules for assigning language and script. In the FDK 2.0, the default languagesystem is "DFLT dflt"; in the FDK .16 it was "latn dflt". For making a new font, you should specify both language systems:
languagesystem DFLT dflt;
languagesystem latn dflt;
If none of this helps, send me the old and new version of the font, and I can look into it.
- Read Roberts