I am having this exact same issue. I run a crap ton of mods but the ones we have in common are B9 aerospace KAS Kethane KSP Interstella KW Rocketry MechJeb2 Scansat This problem is getting really annoying everything seems to be working fine and then the buttons just stop working. I don't notice it until I have to click on recover vessel then nothing happens and im usually on the ground by then. I try to EVA to see if it will work outside but as soon as I do that Jeb comes out and I cant move him or let go of the ladder or anything. So I try to recover vessel or go to space center or even revert launch and nothing happens, if I rageclick the buttons they say "No target". Really weird hope someone can come up with a quick fix.
