I started a new sandbox game, started with a mk1 pod, slapped Engineer7500 on it and started building; adding parts (stock only, though I do have mods installed; looking at the craft file, at least KAS adds some modules), altering staging, switching reference bodies, mostly between Kerbin, Mun and atmosphere/no. 10 minutes later, KER froze. Craft file. I have a thought. If you build a rocket large enough (not really large at all by my standards, see craft file above) with one reference body, then switch to another reference body, KER will hiccup for maybe half a second calculating the values. If at this point in time, before KER shows the updated new values for the switched reference body, you switch reference body again, it freezes. I think that's what caused it on this test at least. There may be a separate bug that has the same effect, though, since I've had this freeze while adding parts as well. (though you may have fixed that one, don't know)