Measuring the inter-winding capacitance of a multi-coil transformer
There are two common ways that transformers are wound. The first method, which is typical of power transformers, is that each winding is a separate layer. In this setup, a winding will have significant capacitance only to the one or two windings immediately adjacent to it. It will essentially be electrostatically "shielded" from the other windings. In order to figure out the construction of such a transformer (if it isn't otherwise obvious), I would ground all of the unused windings when measuring the capacitance of a specific pair. Then you can infer the sequence of layers from the pairs that show significant capacitance.

The second method, which is typical of signal transformers, is to use a "multi-filar" technique in which all of the windings are twisted together and wound simultaneously onto the core. In this setup, the mutual capacitance among any given pair of windings will be the same as any other, which simplifies the measurement problem.