Having just gone through the whole thread on limestone and the orange stains, I would concur that the most likely driving mechanism is the migration of an alkaline solution from the fresh mortar.  Whether it is dissolving iron minerals (which could be present in very small quantities) or organic substances, I cannot say.  I suspect that the only way to determine this would be to get some stained material and have it analysed for organic compounds using a solvent extraction process (or alternatively do X-ray diffraction on scrapings from the joint ... but this will not pick up organic compounds, only inorganics).

Alternatively, I will try and find an email address for Bill McDonald, who spent many years as the public face of the Indiana Limestone Institute, and who is pretty clued up about that material.

Cheers

david west