I am having the same problem.
I am using a custom airframe - UGV - and have tried many different mixer combinations and continue to see that when negative values are given by the RC controller the PWM out does not reflect those values. This only happens on the throttle channel, other servos and channels respond as expected. I have tried multiple mixer control groups including the straight passthrough which also did the same thing.
I have also tried incorporating VTOL attitude control, specifically trying to get the VT_B_TRANS_THR parameter as in the text it says "3D ESCs assume 0 thrust at 50% throttle, positive (forward) thrust above 50% and negative thrust (reverse) below 50%. " and this is exactly the type ESC I am using. Note, no luck with this endeavor.
I am not sure where to go next in trying to troubleshoot this issue. I know I have put in about 20+ hours trying to troubleshoot the issue and would love to hear some other ideas.
I think coreysmiles has it right ->
It seems multiple people are encountering this issue, so any guidance and direction would be much appreciated.