I raised the key one semitone for the sample I took from the video to bring it to a comparable level with my recording. That might have affected the tone a bit though, and I probably should've had left it untouched and re-tuned my guitar to Eb for the comparison instead (because open chords). Thanks for the info about version differences.
Thanks, I'm feeling more confident about my Helix now. I might have overreacted a little to the tone difference because I've been having a little bad luck with faulty products (in general, not meaning Helix or other Line6 products) lately.