if you read around some (not everyone has the kind of time I have for scouring the net for DID info), you'll see that headache of varying intensities (a your mileage may vary- thing) go with switching.
it's pretty common. everybody's different, every system is different. and the possibility it's unrelated to DID shouldn't be forgotten.

For myself, sometimes having more than one part active at the same time, like at a therapy appointment, will leave me feeling semi disembodied and like my head has been pushed all out of shape from the inside. frequently I get an "eyeball" headache, too.
you know, when the ache is behind one of your eyes?
oh, and I'll be exhausted as well.
I've read a few good ideas about why it can be so tiring. like- it's because running multiple identities at the same time uses way more energy than just one. is it true? IDK. but it's kinda funny.

I have had to fight to stay "on top" during a few intense therapy appointments. I have really weird experiences and sensations at times like that. like feeling as though I am upside down suddenly, or like the room is slowly spinning or rolling over, like I am shrinking, and changes in perception. Like things being closer, or father away than they should be. it's pretty weird.

The thing is that it's a completely subjective experience. and there's no way to really share how it really feels other than words.

I still have parts that will not communicate with me. I have some that will do what ever they can to knock therapy off track. I have intense issues with shame over parts being seen, and because I have DID in the first place.
Which I know is not logical.
You sort of have to put aside any thoughts of any of this being logical and predictable and take it as it comes.

I was pretty focused when I started this, but it's gone a bit awry. if any of this is helpful, great. if not? sorry 'bout that

jax