I fixed this by uninstalling FNV and MO reinstalling FNV and MO 1.3.3 and first thing I did was create new profile and make sure archive invalidation was ticked I then moved the fallout-invalidation.bsa into the data folder and everything was good to go this time around. So step one reinstall it all then make sure you fallout ini's are not set to read only then do as I have said and create new profile in MO before adding any mods and tick archive invalidation also sometimes you may need to un tick and re tick just to be safe.
