Thanks everyone for your responses... Sorry for coming back late, was at a meeting all day. In the meantime, I did call back the manufacturer to confirm if the cold water pipe connection affected the machine or vice versa just to make sure.... He said again that it's the machine that gets affected. When I asked for an explanation unfortunately, he wasn't sure how, it's just what he's told by his engineers.
golddigger asked if the vendor asked for a separate earth electrode to the machine... The answer is no. All they say is we can't be connected to the cold water pipe.
so say I use an isolation transformer with an isolated ground going to the machine. Would this alleviate the problem? (If there is one). But I would still have to ground the secondary of the transformer to building steel... Wouldn't building steel be bonded to the cold water pipe anyway, in which case I'm back to square one?