I'll try and recreate the bug and get the log uploaded after a force close, to keep the error at the end of the log. If Horseman gets the bug without Mechjeb, you might be right. Given that the stock command pods are suffering the brunt of the bug, I don't think it will be a part adding mod that's doing this, unless they also run plugins. I've found that it doesn't start to appear until you're a couple hundred days into a save, with quite a bit going on. I haven't had it bug out on .25 until I had a large MKS base on Minmus (which i can timewarp with fine, probably because it's not in an orbit and has no pod), and two craft in transit. Once it starts happening, it bugs out across all my saves, and won't stop until I restart KSP. I'm off to bed now as it's early morning here, but when I'm playing next, I'll try and bug the game out and provide the log. Hopefully someone can find out whats causing it, beyond the temporary measure of deleting Mechjebs cfg files.