Hi there @Janus92!
I switched to the latest SEP version, as well as your script version. Not sure what you did to it, what I can visually notice is that booster landing burn starts a bit later than it used to, but I have this issue when roughly half the time with Tanker and Cargo Starships the booster will miss the chopsticks just by a little bit and drops right in front of the launch pad or at the very tip of the chopsticks and falls off. No issue with Starship Crew, nor with Cargo when launched w/o payload, so I suppose the added weight is the problem. Same with Starship Depot. Earlier versions worked like a charm every single time, but this one has this issue sometimes. And sometimes it doesn't.
I use SEP and SLE dev, no Kopernicus. MechJeb utilities are all disabled. I use stock .craft files. Could you please look into it?