Just wanted to chime in with my experiences as well...
I've noticed this issue, but oddly enough it only happens to be when I do Trial of the Champion and/or Flame Leviathan. It occurs after the vehicle/mounted phase in ToC and after defeating Leviathan, when the server "kicks" you out of the vehicle. My (and my wife's) bindings reset every time. Perhaps it is due to the "bars" resetting? Either way, since we're not jumping into combat right away we usually have time to go through 1-by-1 and rebind all the keys. Luckily we don't use a lot of custom bindings; just the default 1-=.
I will try the console command when I get home from work and see if that helps or resolves. It could just be a coincidence that it happens to me on these events, but a coincidence that's happened 100% of time the past 2-3 weeks nonetheless.