Sorry for the delay here. I seem to have lost contact with my own thread. I sent this a few weeks ago in response to your suggestion:

Strange ...

turning on debug

%!TEX Directives: {}

Typesetting Directory = /Users/dcroton/work/documents/current/antonio_agnfrac

master file = agn_fraction_v12.tex

Typesetting Directory = /Users/dcroton/work/documents/current/antonio_agnfrac

Error: Could not open to check for packages

This is most likely a problem with TM_LATEX_MASTER

Thanks, Darren