Only guessing... There is an confirmed issue with the receiver EQ using more than one slice, could it be the same thing you see? Try to change mode i.e. go from LSB->CW->LSB and see if the EQ do kick in.
TX or RX not working? just checked here and at least with a windows slice up and a IOS slice up the RX EQ works on both devices here. I haven't tested the TX EQ but have not noticed anyone complaining about my TX audio going wacko if I have someone connect in to the Radio. BUT I always do a hard reset anytime I do a firmware upgrade. good luck 73's Bret WX7Y