I just got done watching an episode of Secrets of the Dead where they were arguing for syphilis being an Old World disease. They brought up some good points but I still found the various hypotheses to be…lacking (but then again, they only have an hour to condense things down for the layperson, like myself). The main thing I want to know is, are there other diseases that leave lesions on the bones similar to syphilis?
Yes, a number of other diseases are associated with bone lesions that resemble those of syphilis.
I suspect the program you saw concerned this article: Two Probable Cases of Treponemal Disease of Medieval Date From England (by Mays, Crane-Kramer, and Bayliss). I was able to locate the article on the internet but am unable to link to it. Regardless, the authors devote an extensive fraction of their manuscript to a “differential diagnosis” of the lesions (i.e. a consideration of what else the lesions might represent such as Paget’s Disease, osteomyelitis, yaws, and other assorted infections) and make quite a convincing case (IMO) that, indeed, the lesions are syphilitic in nature.
Yes, I think that’s the one. They dug up the skeleton from a friary. I’ll have to try to look around for that article, thanks muchly 
Further in the program though they were showing other skeletons from Pompeii and a Greek settlement in SE Italy that they also thought were syphilitic.
I was only able to access it through my university’s e.library (which has a subscriotion for on-line access)
Yep, I have to go to my old JC here pretty soon to work some things out, so I will probably pop onto EbscoHost while I am there.