Font Only Works Once

I have created a font, and am using it in an application that I have created that generates PDF files. The primary purpose of creating this font (and purchasing the software to begin with) is to be able to support characters commonly used in mathematical equations. I have found that this works properly in the first document that is generated in my application, but in each subsequent document, many of the mathematical operators are not found (and display the not found character). This only seems to happen within my PDF generating application. I have no difficulty whatsoever in using the font in standard word processing applications. Is there anything that you can think of that would account for this?