Make sure you don't have AX8-Edit running. It will cause additional delays and glitches when changing presets or scenes because it's polling the unit for all of the parameter values to display.
Looks like a lot of your X/Y changes use the same models and have minor changes. Use scene controllers instead to change the parameters directly and it will be totally seamless.
You can assign the same scene controller to several different parameters at once, even in different blocks. If you set the scene controller to either all the way up or all the way down for each scene, you can then use the MIN and Max values of each parameter's modifier to set the desired value for each state. Because each parameter has it's own modifier, the same controller can supply very different values as you change scenes. Min is the value used when the controller is at its lowest and Max is the value used when the controller is at its highest. Min can also be higher than Max to make the controller work backwards as well. For change combinations that are always used together, use the same scene controller. This all works the same way for the other controller types as well (LFO, Sequencer, External, etc.)
For example, say you want to get a clean and a dirty sound from one amp. Assign one of the scene controllers to both the amp gain and output volume parameters. For scene 1 set the controller all the way down, and for scene 2 set it all the way up. In the modifier for the gain parameter, set Min to a low value for the clean tone and set Max to a high value for the dirty tone. In the modifier for the output parameter, set Min to the output level needed to make the clean sound loud enough and set Max to the output level need to make the dirty sound balance correctly with the clean. If you have effects parameter changes that are used only with one tone or the other like delay levels or feedback or whatever, you can assign those to the same scene controller as well. There's only two scene controllers, but you can have each assigned to a dozen different blocks and parameters using this method.