Odd... nGCD in default configuration should be compatible with any race mod. Some of the advanced settings can assert assumptions about average/baseline attributes, but unless you've enabled those I can't think of anything that might break it with regards to racial stats.
Here's an idea, though. What result do you get if you type this at the console:
GetGS fPCBaseHealthMult
When I said it doesn't happen with a completely new game, I meant a vanilla game without OWCND. It only happens when OWCND is loaded.
You may be aware that this overhaul has conflicts with a few mods such as Hud Status Bars and Oblivion Xp Updated due to the fact that it uses a different menu structure from other menus.
Also, I have found that a red mist effect when you die using OWCND no longer happens if you use another menu such as BTmod. (Took a while before that penny dropped!) But I hasten to add that I do really like the OWCND menu - svcker for punishment!
However, despite these conflicts, I have no intention of giving it up, as it is my favourite overhaul by far - and I've tried them all!
In answer to your question, I got the following result:-
gamesetting fpcbasehealthmult =1.00 with nGCD running.
I should add, that in order to use a levelling mod other than OWCND's in-built one, you have to switch OWCND's off, which I have done any time I've tried nGCD.