What is the source of leakage current thru an isolation transformer?
There are a couple of things going on here.

First of all, many isolation transformers do NOT isolate the ground terminal on the load side; they simply connect it through to the ground on the supply side. I've never understood this reasoning, but there it is. This means that the input ground of your scope is still connected to the building ground even when using the transformer, which sort of misses the point.

The second thing is that unless the isolation transformer is built with an internal electrostatic shield, there is capacitive coupling between the primary and secondary windings, which can easily pass the 29 &micro;A of current that you're seeing. This is why if you measure the voltage between either terminal of the secondary and the building ground, you'll often see a reading of about half the line voltage.