KerbMAv,. I'm having a similar issue. Anytime I quick load or switch to the space center and back to the vessel all the parts are missing except the capsule, my kerbal in the lower right corner is gone, and the "ship" freezes in mid air. I have many of the same mods you do. I'm in the process of narrowing it down, I've removed all my mods and I am adding them back one or two at a time until I find the culprit. I'll let you know what I come up with. I'm at work now so it won't be until tonight. Edit: Is the issue in this thread the same as you're experiencing? http://forum.kerbalspaceprogram.com/threads/96082-Ships-suddenly-stop-functioning-fly-apart-Mun-clipping-0-25