Ok, I think I'm just going to give up on the Deactivating Abilites part, in part because I just can't figure it out but also because I'm not sure that the ANE version of the Allergy Hindrance should actually affect ALL Super Powers anyway. After all, if you have some powers in a Device does your Allergy affect those as well? (In other words, if Superman had a stun gun, would Kryptonite prevent his Stun Gun from working?) Or maybe vice-versa, what if the Allergy is for those things in a Device, so let's say if Namor were flying around in Iron Man's suit, but the suit he had has an Allergy to water (it wasn't waterproof, in other words), would Namor loose his super strength because of the suit's allergy? I'm not sure if there is an official answer for that, but I figure it's better to leave the flexibility of leaving it to the player to deactivate only those things affected by his Allergy.
That being said I still can't see what I'm doing wrong with the first part of my code above.
The way I read what's happening is that I set a modifier variable to equal 4, then I check to see if the user has made this hindrance a Major Hindrance and, if so, I change the modifier to equal 0.
Next I check if the Allergy have been Activated by the user. If it has then I apply whatever my modifier is to all Skills and Attributes, which should mean at a Minor hindrance I'm applying a -4 modifier, but if it's selected as Major I'm applying a modifier of 0. Unfortunately when I select it as Major I'm still getting a -4 being applied.
BTW, since Mathias mentioned using just SPCPower above instead of component.SPCPower I tried that syntax with the component.Skill | component.Attribute line as well, but it gives and error of that being an invalid tag expression. Just as an FYI, so I'm still using the component. part.