This was something that I did actually have to re-check and I am running the correct loader. I have the GOG version of TES4 Oblivion which at the beginning of my modding session, I was not aware that that version of the game had its own obse loader. So I did have to redo my obse. But I was still missing mods in game. Eventually what I was able to do is simply play the game and just pay attention to modifications that I know I installed with OBMM but were not showing up in game, and then just re-install those missing mods. This process has actually been working rather well so far and I have been able to salvage my gameplay. I should also mention that another problem I was noticing was that some mods I was trying to use were showing up with black squares in the OBMM app. I made a few attempts to re-download and re-install these mods but in the end I just removed them altogether as they weren't all that essential to my gameplay. A few of those black square mods were MeteorShowers - https://www.nexusmods.com/oblivion/mods/15377 / the Midas Magic mod including the omod version of the mod - https://www.nexusmods.com/oblivion/mods/9562 / omod Midas version - https://www.nexusmods.com/oblivion/mods/18507 / Harvest Flora - https://www.nexusmods.com/oblivion/mods/2037 and Mike's Clothes Replacer v1.1 - https://www.nexusmods.com/oblivion/mods/7487 . There might have been one or two other problem mods that kept showing up in OBMM with black squares but I don't recall what they might have been. Anyway, I have had a fairly successful time re-installing mods not appearing in my gameplay so far. I guess I would say for those GOG Oblivion gamers, when you start a modding session, maybe check to see if you need to do a Verify/Repair option for your Obliviion game in the GOG launcher after you install every 10 or 20 mods. If you do need to Verify or Repair Oblivion, run the game to see if your installed mods are appearing. If they don't then you probably need to simply re-install the missing mods and it should work. So I still don't know what or why performing a Verify/Repair of Oblivion would cause or if in fact it did cause some of my mods to not appear in game. At any rate, like I mentioned, I have been able to salvage my modded game.