Alright, so I've essentially ran into a wall with this issue. It seems that the Creation Kit can only edit forms that are form version 40 or lower. Any form set to 43 (the current standard as of, I believe, 1.6 and Dawnguard). The Creation Kit simply refuses to edit these forms, in my case it's spitting out the error of "[form name] is a different version than when it was loaded. Check out prevented." and does not let me alter that object. This is a problem, as the CK seems to be randomly changing cells and even my worldspace itself (which isn't so much of a problem right now, it simply is preventing me from changing the cloud mesh).
The authors of TES5Edit released a script that changes the from version, but changing it back to 40 results in a bunch of data truncation errors upon loading. Do you guys know of any solution that allows the CK to edit form version 43?