Per the Nexus site, the author of FOMM is no longer actively supporting it, and I vaguely recall reading that a game patch caused archive invalidation in FOMM to no longer fuction correctly. Does that sound correct?
I'm using FOMM, but not all of my new textures were getting into the game, so I ended up going old-school and actually built an ArchiveInvalidation.txt file to get things to work properly.