Don't know if this'll help, but I had the same problem abit ago, and what I did first was update NMM to the latest ( if it wasn't already), and when it starts if it asks you about a file having read-only on/off, let it change it. After I did this most of the mods were staying checked but the ones that were installed in-game (with the in-game mod browser), kept unchecking. To fix this I had to delete all of these mods ingame, and then find the normal version on this site (or whereever else they are) and install them through NMM aswell. If NMM doesn't tell you about changing read only options, then go to the ini files (specifically the plugins one you said about) and check to see if it is read only. If it is, uncheck it then let Loot reorder the files again. It *should* work. (After this, it should be alright to make the file read-only again, if you'd like)