BRUXXUS

Yup! I solved my issue a few days ago. It had to do with the virtual install and the fact that my mods were on another hard drive and I didn't have multi hard drive setup. I'd recently moved my FO4 to an SSD and left the mods on the HDD. I could have sworn it still worked until the recent NMM update, though. What I did was change the mod installation location to a new folder on the same drive the game is installed on. NMM automatically uninstalled all the mods and reinstalled them in the new location. It was really easy and cool that it did all the work for me. Everything working great now!

Same here. Some work, some don't. I installed a player texture mod manually, then installed another one that should have replaced it. NMM didn't ask me what files to replace, instead it just deleted everything in the folder... something is wrong with the newest version.