Hi Stefan,
Very strange.
When I first got the loco, I could see a clear difference between running digital and analog. In digital the stutter was very noticable, and it seemed that it was very sensitive to dirty track. In analog, there was less stutter, but it was still present in a subtle way.
Then I started experimenting, and I discovered that disabling Railcom protocol on the control central, on my Ecos (so not on the decoder!) made digital and analog operation have the same subtle stutter. Please try to disable railcom on the control central if you have the option. Either see whether you can improve by disabling the Railcom protocol, or if it is disabled already, if you can make it worse by enabling it?
This leads me to believe that bad electronic design is the cause for the bad running, so nothing mechanically and no dirt either.
Then I added the capacitor as described. That basically fixed it for me. Maybe worth to mention that I have one of the very early Ecos1 centrals with a fixed power supply voltage of 19V. Maybe voltage level has to do with it as well? Can you try the original the original decoder with the cap and without resistor/diode? Thats how I use my loco. It could also have to do with the quality of the cap, like its parasitic resistance. Maybe the sinus driver demands current from the cap in short spikes, that will cause voltage drops over the parasitic resistance. This is all just guessing but it might be worth it to try another cap as well, and do use premium caps. I am convinced that with the right recipe your loco will be fixed too.
I have railcom permanently disabled on my layout, as it makes most locos with older decoders and without powerpacks run worse . No wonder, railcom inserts short 'gaps' into the trackprotocol where all power from the central is cut, for the decoders to talk back to the central. This gap has to be bridged by the decoders always, and makes locos behave as if the track is dirty all the time.
About the red leds, no I havent tested this. If they would be present, would it be possible to enable them with the original decoder?
Bert