Keep in mind if it is script related even after deactivating the mod that is causing the trouble, there might still be scripts in the save you are using.
If you are unsure as to which mods are doing what to your magicka then unfortunately you will have a long effort deactivating them and checking. That is of course a highly simplified description of what I reckon is happening, but you get the picture. ModB did nothing however and ModA's nerfing gives a negative result. ModA thinks it is after ModB and therefore nerfs the magicka to be at the correct level, because it thinks ModB boosted it. I would agree with that it is most likely a scripting error, possibly based on an incorrect order. This would seem to indicate the problem is not with any vanilla assets or code but rather with how one or more of your mods is working, or more importantly - not working. I tansferred that save to my modded profile and while all the mods were being registered the Magicka drained down to -75.
I got into helgen keep and my Magicka seemed fine.
