I am working on a Bible project (http://peacebyjesus.witnesstoday.org/New_Testament_TOC.html) which incorporates many cross references and Bible refs, and RefTagger is a real blessing in it, thanks be to God, but after doing Matthew thru Luke i found out that RT does not not tag certain abbreviations such as used by E-sword, which can be seen here: http://peacebyjesus.witnesstoday.org/Abbrv.html
As a result i used a search and replace software to replace the missed abbreviations with ones that work and i hope it did not change actual words (like Pro to Prov)!