The howlers that I have that are 6"+ in length are either horn howlers or the Red Desert Howler and the Primos Hot Dog. I have a hard time howling with the Red Desert and the Hot Dog with their small, long barrels. So I made a shorter barrel that has a larger diameter exhaust, and the Red Desert mouthpiece sounds great in it. I called in a lot of coyotes with that howler before I got my Cronk buffalo howler.
I haven't made a howler that has a long barrel similar to those two due to ease of use problems that they have. I have heard lots of folks have issues with those long skinny barrels, so that's why I kind of have shyed away from them. My guess is that you are running into a backpressure issue on the barrel due to the length of it. The Red Desert toneboard has just about the largest air channel and exhaust that I have seen of any toneboard, and it has issues with that long barrel.
How long is your howler toneboard? The longer the toneboard, the easier it is to get consistant howls out of it without those tone breaks.
Brian