Maybe they can fix it with a firmware update!! Fingers crossed, if they can control input impedance via software. I think they let each effect block simulate its original input impedance on some of there digital effects. Did the dude doing the actual measurements (thanks by the way, @ben_craven), try different effects for the first effect block?
If this turns out to be a design oversight, line6 could make it right with a low cost hw input buffer. It could plug into the guitar input socket with a 1/4 " input of its own and use a pigtail power off the main power jack.