Adar:
As bigamp stated, it does appear that something is not right with the installation. The problem will not be resolved safely by disconnecting the transformers from earthing...
there are several reasons for grounding (earthing) the transformer -- foremost is safety -- however, failure to maintain that ground with solid continuity throughout creates a hazard...
1) have you done a voltage check between the operator's (start/stop) stations and a solid ground? also to the ground connection in the station? check for both AC and DC; check for both 120v as well as volts < 1 volt... check it to the floor..
2) since these are non-conductive (or supposed to be)stations, is there a chance your operators are building up a static charge? I would assume there is no carpet and the floor is typical industrial (no special coatings?) what type of equipment is nearby? anything like capacitor banks that would induce a capacitive charge?
3) check your ground connections -- does it use conduit and / or cable trays for its earthing? are these properly bonded or has time / plant mods made your connections have an impedance and not adequately earthed?
4) has the building structure been properly earthed? (so there is no potential between the floor and the equipment that may be properly earthed?)
5) check out any lighting circuits in the area for any paths to ground -- these sometimes may not have a solid enough ground to operate a breaker, but sufficient to create a step potential under some conditions and a shock. Is all the equipment properly grounded (for the same reasons)...
6) take a hard look at the wiring to the stations themselves -- is the insulation good, are the wires properly terminated, are the switches in good shape, is the ground connection properly bonded to earth?
7) how old is the plant? what type of soil conditions are present? what type of materials / chemicals are used, etc? has the plant ground to earth be checked lately to verify that it is adequately grounded?
8) is the control transformer properly grounded?
9) regardless, the operators are right about bringing this issue up and it needs to be resolved...
sorry about using the terms earthing and grounding intermixed... I am used to the term grounding and not earthing...