After some testing the culprit was found. It was the J. Rockett Archer Ikon. After contacting Surfybear someone there explained how the decay circuit works and that loud signals could mess it up. A short search on the net showed me that other people had issues with the Archer messing up digital pedals sometime.
I checked the signals with my scope and the Archer puts out a huge signal when bypassed but it is such a high frequency that you can't hear it. The only thing that could be the reason was the charge pump. If you look at the pictures you can see that the pcb track on the left which carries the input signal passes the charge pump very closely.
You can see my quick and dirty solution on the picture as well. I desoldered R1 (10k) and the pin of the input jack and put a shielded wire from the input to the capacitor (. 1) via a new 10k resistor. First I took an unshielded wire and soldered it to on of the pads of R1 which did not work and I lost that pad in the process but the pin on the capacitor works better and using a shielded wire got me rid of most of the charge pump noise. Now decay works like a charm. Since other people had issues with that I thought I'd post it.
To do it properly one should probably cut the track from the input jack. I just sucked out all the solder but it can still get contact which it shouldn't.
So if you got issues with your Archer maybe that could solve it.
And if you're using a charge pump on your designs you should probably give it some space.
Unfortunately the picture of the whole pcb was too large to be uploaded here and my phone didn't let me alter it. I will upload it as soon as I can. If someone is interested...