Is it perhaps locked in an active state?
IOW, check to see if the slot it's in is locked. If it is, powering down and switching the unit back on will simply restore it to this last-used state; it'll change nothing in this regard.
Locking survives a power cycle.
I guess, you need to first explain your intentions.
How are you planning to activate and deactivate your wah effects?
Via Rig change, via toe switch (the Mission EP1 is available with and without toe switch) or via Pedal Mode in each wah effect e. g. Bypass@Heel?
I have mine set up with a Wah permanently locked in Slot B and the tow switch of the Mission assigned to Toggle On/Off Stomp B. It worked fine go a long while but recently it has started powering on with the Wah active even when inactive on power down. I just assumed I have done something stupid and haven’t managed to trace it yet. When something like this usually happens to me the cause is normally my own stupidity ?
However, maybe this time there has been a bug introduced if it’s not just me. I still think the most likely reason is something I’ve tweaked by mistake so I’m going to continue monitoring it myself.
It's a pity one cannot lock independent slots. It would be nice to be able to lock just one effect in one slot while others change depending on rig.
You can lock module by module and section by section.
Ooops you are right!
I’ll check it out when I get back home after the weekend but I don’t think I’ve locked any slots. I use the toe switch on the Mission pedal to activate/deactivate the wah. I tried reversing the polarity but that had no effect. After doing that, though, on the nex power up, the way was on as usual but as soon as I moved the pedal it turned off.
This exactly happens to me and with the troubleshooting I have done it seems that the Footswitch assignment is causing this. And definitely seems like a bug.
When the Kemper boots up all is Ok as it should. However, as soon as the Remote finishes booting and connecting, the Wah or whatever effect is on Slot A (footswitch assignment) on whatever patch happens to be selected, gets enabled automatically. So it appears that the remote sends to the KPA a footswitch press action. I am using a TS cable with the Mission EP-1.
This is easily replicable Burkhard
I sent a back up of mine support and we couldn’t find the cause. However, after a bit of tweaking I managed to solve it. Not sure what the real cause was but in my case it got sorted by changing the type of pedal assigned to the slot. I turned the pedal type from Mono switch to two way switch then Kemper pedal then back to Mono Switch. From then on everything worked fine 
I can only presume the unit was stuck in some sort of software loop or something. Pretty strange and I can’t understand it but it works fine now so I’m a happy chappie 
New Kemper owner. First time poster. I have this same issue, if you want to call it that. I find it to be only a minor inconvenience. I have a Mission EP-1 connected to the Kemper foot controller. The switch is connected to port 5 and the pedal to port 6. I have the jacks set up for 5 - switch and 6 - expression. On those profiles that I have a wah assigned I always do so in Stomp slot A. If I boot up the Kemper and the profile on boot up (the last one I used) has a wah assigned in Stomp slot A it is engaged as soon as the Kemper completes boot up. I have not moved the wah to other slots to test them. I simply turn the wah off and carry forth.
It's worth mentioning that in my setup my cable connecting the Mission EP-1 to the foot controller is a Dual TRS cable, meaning both sides are TRS. Using a TRS where you only need a TS should not pose an issue. I had assumed that my use of a TRS for the switch connection might have been causing my glitch but after reading this thread I doubt that this is causing it on my system since others are experiencing it, as well. Otherwise it functions normally. I use a Dual TRS cable since that is what I had on hand.
Edited to add: I just tried the Mono/Dual/Profiler switch setting advice in the post above and that seems to have solved it. Thanks!
Edited again: I spoke too soon. I had not waited until the controller was fully booted. Still doing it.
Have you checked the polarity for the pedal. I think the Mission Switch needs to be Inverse. In my case it wouldn’t even let me change the polarity until after i changed pedal type and back. After that it let me change polarity and everything now works fine.
Good catch. I set the switch polarity to inverse and that seems to have cured the issue. Many thanks for the guidance.
Glad you got it working.
