I have Basecamp on windows XP and the Mac. On XP I was getting the message about userdata.gpx being missing or not being able to read it. I also have problems that none of the maps on my SD card appear in Basecamp.
I don't think these are related. In fact I don't think the userdata.gpx message is anything other than a harmless warning.
However, you can create the file quite easily. It's where Basecamp writes tracks and data to if you transfer them to the SD card. So select a track, waypoint or list and send it to the GPSr selecting the SD as the destination rather than the base unit and you'll get a userdata.gpx created for you.
Net time you start basecamp the error/warning won't be there.