What are the reasons for negative gap voltage in vibration probes?

it depends on each probe setting . most of probes have negative gap voltage because its represent the distance between the probe and the surface that it observe . as this distance increase you will find the gap voltage increase as well 

nothing special. they discovered later it can be positive gap voltage but it will require 2 product lines , one for negative (spares) for the existing parts and a new product line for the positive gap ones