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Fallout will not load mods


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I've recently been experiencing some very strange problems with Fallout: it started earlier this week with the game loading mods that weren't selected. FOMM would have them unchecked, but in game the corresponding quests and content would start up no matter how much I struggled to fix matters. After a few restarts and a lot of cleaning in FO3Edit, the problem seemed to go away...

 

Except now Fallout doesn't run anything but strictly vanilla content. I've checked the mods in both the standard loader and FOMM, I've verified that plugins.txt is listing the desired mods as active, I've re-installed the game repeatedly... no dice, it still starts up with only vanilla running (both FOSE and non) no matter what I do. For someone assisting with a few mods and working on their own projects, as well as heavily relying on modified gameplay to enjoy their Fallout experience, this is a deal-breaking problem. Does anyone have a guess at what else I can try to take a stab at getting things working correctly again?

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one quick question is ArchiveInvalidation Invalidated still on ? also FO3Edit is good but sometimes it can mess up all your mods, breaking them all try redownloading new one and see if they work...
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Yes, I've toggled ArchiveInvalidation repeatedly.

 

As for FO3Edit, that tends to only be an issue with the MasterUpdate function. Judiciously using it to clean up unused entries and conflicts can't really mess with everything across the board.

But to keep up the details on what's going on, I have repeatedly re-DLed some of the mods I'm using to see if Fallout would recognize the new copies. Same result: mods are selected and show no issue, but Fallout runs as if it's using Fallout.esm and nothing else.

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Already using the latest beta of FOMM, already re-installed it twice while trying to work out what's wrong. Unless someone has a clever idea that doesn't involve repeating the same actions over and over in hopes of a change, I guess I'll just see if there's anything suspect in the registry. I'm not too hopeful of that, but it's all that would seem to explain an issue so persistent that re-installing on a new machine seems like the only fix.
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