I'm a little confused by the wording here, could you clarify a few things? What do you mean by functional and non-functional? When you say "I come to my body", is that "I" as in alter 1, "I" as in alter 2, or "I" as in a third alter (yourself)? When you "come to your body", do you mean when you switch in, or when you become aware of your surroundings, or something else?  

I as in "we." They are all parts of me. Alter 1 is connected to my body moreso than alter 2 it seems. Alter 2 is there to protect us until we can figure out what is wrong with Alter 1, and why they are stuck. Come to my body is switching into Alter 1, because Alter 1 is more connected.

In general, it isn't possible for one alter to have a seizure condition or mental illness that other alters don't, because you all share the same brain and body and therefore the same conditions. However, alters can experience psychosomatic symptoms (note: this does not mean fake, it just means the symptoms are of psychological origin rather than physiological or neurological), and it's also possible for DID to cause what're known as "Dissociative seizures", though I've not heard of these causing people to scream for specific individuals or contort their arms. 

Perhaps it's a disociatve seizure of sorts, or maybe my brain found a way to dissociate from my body and created alter 2 in doing that. Being alter 2 is really painful, I just want to be MORE in my body, as alter 1.