At some point in one of my playthrus this stopped working and the Mutant items lost their map markers. Not sure why. If it happens to you the solution is to restart the mod it depends on, Discover Nearby Collectible Items.
The instructions are on that mod's page, but I'll post them here too. Doing this got the Mutant markers working again for me.
Console commands to turn off/on and reset the mod at will. (Don't worry, it only resets the mod, not the items).
CQF SC_Handler ShutDown ===> Shuts down and turns off the mod StartQuest SC_Handler ==> Turns the mod back on (while resetting it)
Just a heads up, schematics don't get map markers. If I didn't already know about the fishing pole at one of the piers around Sanctuary I would have missed it.
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The instructions are on that mod's page, but I'll post them here too. Doing this got the Mutant markers working again for me.
Console commands to turn off/on and reset the mod at will. (Don't worry, it only resets the mod, not the items).
CQF SC_Handler ShutDown ===> Shuts down and turns off the mod
StartQuest SC_Handler ==> Turns the mod back on (while resetting it)