I am having the above problem on texmacs 1.99.1 (and Mac OSX 10.8.4).
I have the box ticked in Prefs > Convert > Latex (Enable conversion of user defined macros)
but nothing happens. I have my macros in a .ts file which are picked up on screen but perhaps the converter cannot find it? Where will it look?
I get in the latex preamble some texmacs macros correctly converted, but not my own.
Any suggestions?
With best wishes,
Philip Welch