It might be worth analysing recordings of a good piper or two playing in E minor and in G, to see if they squeeze the B that little bit harder in the minor tunes, to bring it more in tune with the E/B drones.
They may not do it consciously, but the B that's a true third above G is a bit below the one a true fifth above E; at least if the fifths from G to D, D to A, and A to E are tuned (almost) justly, which you need for playing in G D and A minor. Squeezing a little harder could easily compensate this. John -- To get on or off this list see list information at http://www.cs.dartmouth.edu/~wbc/lute-admin/index.html
