The calculation for the tool height was wrong. If the end mill was actually 50mm long it was reporting something crazy like 500mm. But this issue was corrected. For ProbeBasic to calculate tool lengths you need to touch off the spindle nose so it knows the distance of the spindle to the touch plate (let’s call this distance S). In ProbeBasic S is known as the spindle zero value. Then when you touch off a tool it calculates how far in the Z direction it moved (let’s call this distance M). The tool length (L) will be equal to S - M.
Is that helpful at all? Maybe if you elaborated further on your issue I could be more help.