Chris,
What is the time period on your building? I agree, most likely what you are
seeing is some type of iron oxide pigment in the mortar. If your structure is
pre-1900 you are more than likely dealing with soft lime mortar. If you would
like you may send me a small sample of the mortar and I will be able to tell
what you have. Just send me an e-mail and I will give you my address.

Steve Elkins
Savannah, GA.