The default Zen Cart install sets up an automatic added packaging weight of 3 'units'. In your case actually 3kg, since the Royal Mail modules calculate in kg. So the shipping weight of your 0.001'lb' item is calculated at 3.001kg.
Change it in Admin-Configuration-Shipping/Packaging section Package Tare Small to Medium. Default is 0:3, which means 0 percent, 3 units. 10:0 is a better setting for testing.

Zencart does not do any weight conversions, it doesn't care what you call the units, so to change the units you simply need to edit the files, and change lbs. to kg. Easiest way to find out where is to read the tutorial

https://www.zen-cart.com/tutorials/i...hp?article=204