OK, to anyone who has this problem.
CitizensOfDream was right it seems to be a problem related to certain USB controllers.
So the solution is in this thread
Aircuts on Mach3 USB NcUsbPod - AutoLeveller
There are a number of solutions presented over there.
By "steamer" however I directly tried the solution posted by user "Renato" where he added a dwell time before the G31 probing command
like this
G4 P1
G31 Z-5 F100
So following this I just did a find and replace of the probing lines.
In addition I changed the probing depth from -1 to -5 as shown. so instead of G31 Z-1 F100 I used G31 Z-5 F100
Hope this helps.
Many thanks "CitizenOfDream" for your advice its highly appreciated.