I think this might also be a little puzzling for you Richard as you might not be aware that by pressing each Pedal you can also get it to affect the other switch. So I hadn't given much thought to these really but I now know in order for it to work properly, I need to have Pedal 3 programmed in such away that when I activate it, it will not affect Pedal 4.
This would mean then if I have all presets programmed to have only SW2 from scratch that when I hit pedal 3 I will then end up with SW1 and SW2 on which is a combo that means we will get clean.
Then in order to get the distortion channels I press Pedal 3 again to turn off SW1 and again have no affect on SW2 and as that was already on then we will be left with Ultra.
So in order for Pedal 4 to work properly also it needs to be switched to only affect SW2 and not have any affect on SW1. This way then I can switch between Crunch and Ultra.
So where I think things where going wrong before was I had Pedal 4 programmed to turn off SW1 when I pressed it, which mean I was getting SW1 ON and SW2 OFF at one press and SW2 ON and SW1 OFF at another press and that basically meant I got clean and Ultra only.
So by taking away Pedal 4's SW1 OFF instruction you can flick through the channels if you use Pedal 3 to basically change to clean and use Pedal 4 to go between Crunch and Ultra.
Pedal 3 = Clean/Distorted
Pedal 4 = Crunch/Ultra (but only is Pedal 3 has turned off SW1).
No I have not put this into practice yet as it had only dawned on me when I had left the practice room, but I figured it out when I got home and thought why does one cable in SW2 work Crunch and Ultra but when I plug in the cable into SW1 as well I got back to clean and then looked at how I had it programmed. So I have to make Pedal 3 and 4 only operate each respective SW.
Also to refer to your thoughts on patches taking precedence, well I have the patches programmed in a way that they have no affect on any of the stomp box Pedal 1-4 but also will turn off Pedal 5 if say I stomp on them. This is because I use Pedal 5 as my Solo pedal and in that it turns on Volume boost and Detune. So technically if Pedals 3 and 4 are on this should have not change if I press the patch pedal again. However this is negated by the simple fact that I have programmed in each patch pedal to always turn SW2 on and SW1 off so I will always be on Ultra to start with.
See below on Preset/pedal 7 SW2 will be on when I press that pedal and SW1 off
Then Pedal 3 has SW2 greyed out meaning no affect and Pedal 4 has SW1 greyed out meaning the same.