In the source code for the markup app, the comments say that if the appropriate libraries are not installed, the filter will fail silently and return the un-marked-up text. This seems to me to be a bad design decision. If the proper libraries are not installed, the developer should be notified right away. Not marking up the text is not what the developer intended and does not seem to be a case of degrading gracefully.
Additionally, I was unable to find this limitation noted anywhere on the Web site. It wasn't until I dug into the source and read that comment that I discovered why my app wasn't working properly.