It looks like I'm not the first person to have notices this, because after I submitted a PR to the github project, I noticed another pull request dating from May that has yet to make it into master.

Essentially what it boils down to is that char on arm systems, in my case the raspberry pi, are treated as unsigned characters.  So right now we have a fix for the hackrf firmware update that only works on x86 systems.   A simple change to the source and sink typecasting from char to explicit int8_t on the lookup table on the source.cc should fix this issue for all platforms.  In addition, I believe a typecast in the convert function for the sink.cc would do it as well but I have not tested it and I don't believe my current PR reflects that either.