I'm not near my Hypercube to checks it's configuration file, but unless it's a typo on the forum I've seen something which shouldn't be there.
In this line;
G31 P50 X63 Y-65 Z1.8
I'm sure the a P parameter is in the wrong place and with a too higher value.
Looking at the advice in the wiki;
1. In your software config.g file input the following G-Code commands to allow the setup to work:
M307 H3 A-1 C-1 D-1 ;
M558 P5 X0 Y0 Z1 H5 F100 T2000
G31 X0 Y0 Z0 P25"
Also that P parameter sets the trigger threshold as it's called, to be a little more sensitive as I think there was talk of the BLTouch giving a very fast signal when it's been activated that the Duet can miss.
The advice from memory was to set lower than 25 so the Duet had a chance to read the BLTouch probe signal when it triggered.
"In both cases
Select probe type 5 (the P parameter in your M558 command), Set the G31 P parameter to a low value, because the BLTouch produces only a short output pulse, which may be filtered out if you use a higher threshold."
So if I'm remembering right, you need to move the P parameter to the end of that line of code and also lower it's values to below 25.
This logic falls in with your issue of having different trigger heights perhaps, possible because the P parameter is too high and in the wrong place.
Quoted text taken from here;