Old FLMM trick !
I used a very old trick which "sometimes" works when trying to get a mod to work in FLMM when you have the problem that i did, I must admit that i had to dig around very deep into the dusty notepads of mine to find this, but it worked and for that I'm grateful.
Here is what you do:
1, Complete un-install of FLMM and FL.
2, Reboot comp.
3, Re-install FLMM (v1.3) FIRST !
4, Install your mod into FLMM.
5, Install a clean vanilla of FL.
6, Now here is the trick ... : activate and then deactivate around 4-5 of the larger standard mods you get when you install the vanilla version of FLMM (the larger docking rings etc) ANY 4 or 5 (can repeat same ones if necessary).
7, Try activating CF / your mod that's playing up.
8, Play game.
NOTE:
I just spent all of yesterday testing this out BEFORE i posted here to 1, not make myself look stupid, and 2, because who's gonna trust to guesswork?.
So out of a total of 30 (exact) complete un-installs and re-installs of FLMM and FL this method worked 26 times first try, and out of the remaining four 1 worked when i by accident tried to activate a second time .... 
so maybe (i hope lol) that if i had of tried those 4 twice i may have got a 100% success rate.
Where as before it would not work no matter WHAT i did, it now does and this trick seems to do the job just fine.
/Loves meh notes.
Hyp.
P.S.
Re posted singularly for those with activation problems.
EDIT: add a couple of things to explain more easy and to be sure i was clear ...
