I was in squad with Nivorbian and what he is talking about is this :

You have your armor stats, say 4000 points.
Now the nexus armor module is turned on, this gives you say... 250 extra points.

now say the module is turned off, or you do a save logout.

Now you should be back at 4000 points right ?
But you will see you have 3750/4000 armor, the 250 extra points have become 250 points of damage.

Not sure if this is intended or a bug but imo you should be back at 4000/4000 points.

...edit :

I all so wonder if its intended than when the nexus module kicks in, your max armor goes up but not the armor itself.
In the above example when the module is turned on you will get 4000/4250 armor and not 4250/4250 armor,
must be a pita when you first have to rep the whole squad.