Heyyo,
Yes, new steam update is lame, there's workarounds created by whistler and PODbot mm. I'm sure the fix can be implemented into Joebot as it also uses the HPBbot source code. Check the Joebot section of the forums, I'm sure aspirin's already fixed it.
But not saving or loading waypoints? something's definately messed up with your installation. Make sure the folder's aren't read only, if that doesn't work, try reinstalling Joebot, first uninstall, delete the joebot folder, and try installing again.