I ran your settings here and changing presets generates about 75 MIDI messages per preset change. And, there are duplicate buttons. For example, there are quite a few buttons that control the chorus block, and not all of them are IA Linked together (the way they're configured, they can't all be linked because they don't have the same actions). So you might have an individual effect block turning on and off several times during a preset change. That would cause your problem for sure.If I bypass the iPad altogether and change from the MMGT it's the same behaviour. Let's suppose I decide to change things up and not make use of IA Store but find a different way around. Is the only way to disable all the "IA Store" settings to turn off the "Send CCs on Preset Change"? If I do this, I wouldn't be able to make CC changes via preset actions either, is this correct?
The typical way around this is to allocate some buttons specifically for the purpose of IA Storing them, probably on their own page(s). Make sure that they don't overlap functions with each other (for example, have one Chorus button, or a group of chorus buttons that all work together so that only one button is sending a message at any time). Turn on Send on Preset Change on these buttons. Then, other buttons can be created that are only used "live" and not IA Stored. Turn off Send on Preset Change on these buttons. If you can do that, you'll get rid of conflicts and greatly reduce the number of messages sent per preset change.
I had a look and it looks like "Send CCs on preset change" only affects IA buttons, not preset actions. So you could go that route as well. I don't normally recommend preset actions except in certain cases, but this might be one of those cases.