Just a heads up since I finally have confirmation that this is an issue beyond some quirk of my own PC. If you are doing any sort of work with the official Skyrim DLCs in the CK, make certain the timestamps on your ESM files does NOT go past the year 2014.

For some bizarro world reason, if you set the dates into 2015 (not sure exactly where though) or anywhere in 2016, the CK will load Dawnguard and Dragonborn in the wrong slots and you will be potentially editing things in the wrong order which will lead to bugs, not to mention an ESP with its masters out of order.

I ran into this one myself during the USLEEP merges but though it was a fluke and moved on, but then Pete ran into it as well on his PC which makes it more than just some random fluke.

There's no telling how long this has been a bug in the CK or why it even matters, but it does. This is especially problematic if you need to do a cache validation on your game because it may redownload DLC files and change the timestamps on you when it does.

For reasons unknown, Hearthfire is not affected, but it needs to be dated between the 2 DLCs to load in the proper order. Skyrim.esm and Update.esm should obviously both be dated before the DLCs.

Using Wrye Bash, you can change the timestamps on the files fairly easily. Open it up, highlight an ESP, edit the date in the "Modified:" box. Save the file. You'll want to be sure that when you're done editing, all the dates are in order according to the load order.

Once you have the issue with the timestamps fixed, any mods you have with the out of order masters can be fixed by loading them into xEdit, right clicking on their names, and selecting "Sort Masters". Exit the program once that's done and they should be fixed. Do them one at a time, I'm not sure if the master sorting can handle multiple errant mods loaded at the same time.