This is a long standing issue I've written off as likely not important enough to resolve. My Line 6 gear is probably too old for the updater (Pod XT Live and Tone Port UX2 being the newest, and a couple others - Bass Pod & Floor Board). I just check from time to time to see if a resolution or workaround has been identified, and here were are with workaround steps for the Helix, but I've tried this on several systems from WinXP up through Win10 using base versions, upgrading incrementally all the way to the latest drivers and programs as well as to try the same on clean systems installing only the newest available, installing the very minimum with drivers and programs dating back to the same dates as the Updater version(s) and no method has provided more than a black window with and Account menu, About menu, and white text "Select device to update."
Since the particular version I'm looking at right now is identified through the About menu as, Line 6 Updater 1.16 - using Qt(c) Software under the GNU LGPL version 2.1 (Feb. 1999) license and uses libusb, it may be interesting to explore a bit deeper in Linux (it works as an audio input output device without further intervention, but doesn't have Linux software that can utilize the firmware which makes these devices more than just boxes with extra ports - we love our Line 6 equipment modeling, but it still might be fun to poke around a bit. I haven't had any issues related to the inability to use the Line 6 Updater aside from the Updater issue itself - everything else from the earliest supported software for each device has functioned properly from RiffWorks, GearBox, Pod Farm, Line 6 Edit, Ableton Live, etc.
My advice if it's not crucial to update your firmware: don't stress it and check back here from time to time to see if there has been any progress or if the Updater is retired or replaced (of course unless I'm just not finding a resolution) Sometimes it's okay to follow the "if it ain't broke, don't fix it" path, especially when just about everything works as well as my Line 6 products has been for years now. Rock on!