NMM with SE - odd problem with not launching, and mismatch between the plugins and mods tabs

[el2mador]

Hello.

I have a recent problem with Nexus Mod Manager and I'm hoping you guys can help out if you know how this occurs or how to solve it.

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So earlier today, my computer got unplugged before it could shut down properly. I'm not sure if this was the cause but when I tried to play the game recently, NMM will not open. It just runs on Task Manager for a few seconds then it disappears.

So I uninstalled and reinstalled it.

Upon reinstalling, I was prompted to choose whether I would like all mods to be reinstalled (*"this can take several minutes or hours"*), or for all mods to show up as deactivated (they're still installed and I can activate them later on).

I chose the latter because I guess I'm dumb.

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So now this is how things look like - http://imgur.com/a/U453c

All my mods are showing up as disabled in the mods section; but the ones I had active in a previous playthrough are all active in the plugins section.

I started the game and, *voila!*, my mods are still working - at least for the next few minutes.

I'm unsure if this would cause further issues though.

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(1) Will this end up screwing up my game due to the plugins and mods section of NMM not matching?

(2) Should I do another clean reinstall again and just choose for all mods to be reinstalled as well?

(3) I'm planning to download a couple more mods soon; will this screw up NMM further?

(4) Because my config files were retained, is this the reason why the mods are still considered active and working in my game?

I'm worried of trying to open LOOT because it might mess my settings as well.