Maybe your saddle is too far forward. If it is, he could be swishing his taill due to aggravation or frustration because his shoulders could be trapped. I posted this on another thread, and this is how I place a saddle on a horse.
"Have someone else hold him. With a piece of chalk, mark the back of his scapula (shoulder). Lightly press on his shoulder until you feel it drop off, like the edge of a cliff. A lot of people are told to place the saddle directly behind THIS mark, but it's incorrect. Some horse's scapulas can move 6 inches further back from the resting position! So now, ask him to pick up his leg, bring it to your hip and stretch his leg out in front on him. With your other hand, lightly press around his shoulder until you feel it drop off again. Mark that with the chalk. This second mark is where his scapula moves at maximum extension. You want to place the first weight-bearing part of your saddle directly behind THIS mark. That way the saddle bars do not interfere with his shoulder movement. It gives him maximum freedom of his shoulder.
Now, when you place your saddle in this new position, you will notice that your saddle looks very 'downhill.' This is where SHIMMING comes into play. You will need to shim the saddle up so that it is level. Do you ride western or english?
For shimming material, get some felt that has some 'give' to it. That way when you shim the saddle, his shoulder will be able to press into a soft material, yet still be able to move. You will want to place the shims under the first screw, either on a western or english saddle. It's where the bars start."
Maybe it's possible that your aids to get him to do a flying change, etc. are too much for him. Even if you a soft with your leg, he may need you to be even softer. Try to see how little it takes to get him to do something.