Well there is one possible reason.... Why are you using version 043....
The recommended version tends to be 062 especially with motion controllers
043 was known to have a lot or pirated licences.... When you install the later versions they won't run (correctly) as I believe that artsoft introced occasional glitches into the software that did spurious things.... Like break tools... (Never heard of odd probing though)
You have to remember that the skip signal is very different to xyzabc motion.... Given the servos get given the steps that they need to travel and the following errors mean that it will still achieve those distances... But maybe a bit slower.... The skip motion (g31 probe), means when the skip is triggered motion stops..... A following error means the drive may "try" to continue onwards as the motion lags the steps