Sorry for the weird title but I didn't know how to summarize the problem. I have many vessels that use the Big-S Delta wing since 0.9 or so.
Just to make sure It's not an update issue I rebuild them from scratch. So here's the thing: They work perfectly. Example my SSTO here:
I can fly it into space, save, reload, switch to other craft etc. But when I refuel this plane it explodes the next time I reload the save file.
Let me guess: Invisible struts on the gear?
Because here's the fun part: If I edit the save file and remove all fuel from the wings and the Mk1 liquid tanks on the wings I can load the vessel. It wobbles a bit but it doesn't explode. I can then dock to my space station, refuel it and fly on. As long as I don't change the vessel it works like a charm.