Difficulties in probing

At any rate, here is what I see:

You are using hm2_7i96.0.gpio.001.in for both max-z and float-switch. I cant visualize how you could be using the same switch for both functions, so this doesn't seem right to me. I am fairly certain this is the source of your probing angst.

For your ini file, in the [AXIS_Z] section, your MAX_ACCELERATION should be 1500.0 and not 1000.0 (it needs to be double the value of the corresponding joint. Similarly, in the [JOINT_3] section, your STEPGEN_MAXACCEL should be 937.5 instead of 950.0 (assuming you didn't have it set that way to negate some sort of following errors, etc).

# external input signals

# --- HOME-Z ---
net home-z     <=  hm2_7i96.0.gpio.000.in

# --- MAX-Z ---
# net max-z     <=  hm2_7i96.0.gpio.001.in

# --- HOME-Y ---
net home-y     <=  hm2_7i96.0.gpio.002.in

# --- MAX-Y ---
net max-y     <=  hm2_7i96.0.gpio.003.in

# --- HOME-X ---
net home-x     <=  hm2_7i96.0.gpio.004.in

# --- MAX-X ---
net max-x     <=  hm2_7i96.0.gpio.005.in

# --- HOME-X2 ---
net home-x2     <=  hm2_7i96.0.gpio.006.in

# --- MAX-X2 ---
net max-x2     <=  hm2_7i96.0.gpio.007.in