I just grabbed the Southern Tier GPS data to take a look at it. The download is a single .zip file called stgpsdata.zip. That file unzips to a folder called stgpsdata, which in turn contains a .pdf that explains the files, and seven other folders, named in a format like "ST01v007 Folder" or "ST03v006 Folder". It looks like the folders ending in 006 are from 2009, and those ending in 007 were updated in 2011. The 006 folders contain four files, .gpx, .wpt, .rte, and .mps. While I think .mps is something for mapsource, .wpt is waypoints, and .rte is routes, I'm not sure what that leaves for the .gpx file, but given the relative sizes, it could be a consolidation of them all. The folders with 007 in the name only contain a .gpx file, which has everything consolidated in it. None of these files are empty on my system, so I'd echo Jennifer's question and wonder how you were downloading and unzipping them, since that seems to be where things are going wrong.