When running Line 6 Version 1.12 I was having the same problem -- I got the "Line 6 Updater Quit Unexpectedly" message -- and could not run the program. That was happening because I had my Helix connected to my Macbook Pro's USB port and the Helix's power was on. When I turned off the Helix, the Line 6 Update started fine.
After I logged in, the software asked me to "Select device to update." However, there were no devices listed anywhere on the screen. I could not go further.