Skyrim.esm doesn't need to be in plugins.txt at all. Update.esm loads after all other active masters if it's not in plugins.txt, or in the position specified if it is. The textfile-based standard specifies that Skyrim.esm should not be included, and Update.esm should be included, in plugins.txt
Plugins.text is generated by game isn't it? So, if the game puts skyrim.esm in the plugins.txt then its meant to be there, right? And, then they (Bethesda) leave skyrim.esm out of the launcher so casual don't mess things up.
I set my loadorder by running BOSS and then copying the output into plugins.txt file. I then start Skyrim using the steam launcher and look in the data files so I can uncheck the High-Res DLC's (old machine, not enough resources to run them). When I open the file in the launcher several of them will have been unchecked and moved to below the bashed patch in the L.O. I manually reset these files and then relaunch the game with the SKSE launcher. Is this normal behavior for the setting of L.O. by the game or am I not doing something right? Thanks for any advice and/or clarification.
I think I read somewhere you shouldn't use the launcher in conjunction with another mod manager, but otherwise I was contemplating doing something similar with WB until BOSS 2.0 comes out. I do all the activating/inactivating of plugins (& pkgs) only with WB, and have not had any mysterious unchecked plugins.