Ah f**k it, I'm just gonna start again!
That'll teach me...
Not to rub salt in the wound, but if you're starting again it would be a good time to install Wrye Bash and stop using OBMM. Though it has a pretty steep learning curve, Bash is far superior and has tools that are
required to make mods play nicely together.
With Bash's list of mods it would be easy to pick up on a missing master issue - just look for the big red check box beside a mod.
Not to mention the BAIN installers feature: the important difference between OBMM and Bash's installers is that with OBMM, you install package A, then install package B which overwrites some files from package A. Fine and dandy. Then you remove package B, and the files you overwrote are now
missing from package A - OBMM does not know enough to pull the missing files out of A and reinstall them. You could disable and reenable A, if you knew about the issue, but it starts getting greatly compounded with large numbers of packages. This is perhaps the most important feature of BAIN: being able to "anneal" compromised installs.