I was genuinely confused by this issue you presented to the point where I had to get out my DDJ-RB and actually try to make things go wrong.
The only thing I could come up with was a possible cross-mapping of the MIDI where the LOW EQ from deck 1 is mapped to the CH 2 channel fader.
Start by going into the MIDI panel (button at top right of the rekordbox window) and press the DEFAULT button. It will possibly ask if you want to save changes, say no, and restore the default mappings. Try mixing again, with the MIXER panel open, and see if, when you move the CH2 fader ONLY, anything else moves on the display, or if the issue has been corrected.