Hi again,
So my new cable arrived and I've just tested it out. It's a George L, which seem to be known for brightness. Still has the high-mid roll off. Spectrum looks pretty much the same. So once again at a bit of a loss.
I've messed around with pickup height a lot without solving it I'm afraid.
EDIT:
After playing a little more, I've noticed something weird with the way notes are (sometimes) decaying. When I hold a long note, sometimes as it trails off there is a sudden drop then rise in volume. It doesn't mute, it just gets quieter for a split second before rising back to the previous level and trailing off. Almost like it's being hit with a noise gate briefly, but it's the DI signal, the input gate is off and the stomp gate is bypassed. Not sure if it's related to my EQ woes or not but thought it was worth mentioning.
MORE EDIT:
@Ka5par
Sorry, managed to miss that reply. I managed to find my old Focusrite Scarlett 2i2 today and gave that a try too. There is less of a roll off than the Helix, but still less high-mids than the reference. The 2i2 is also louder, even at min gain, on the instrument input. I found another example comparing the 2i2 to another interface (forget which at the moment) and the 2i2 was noticeably less bright sounding. Here's a Helix/2i2 comparison with my 7 string and the new cable:
Helix:
2i2: