The thing to understand is that the thyroid gland affects the entire body. That's why it's so dangerous to let hyperthyroidism go untreated. It speeds up the metabolism and can ruin all the other organs. Usually, an overactive thyroid is caused by a benign tumor on the gland itself. Add to this the fact that sometimes, abnormal thyroid tissue goes wandering around the body, and it's a tough nut to crack. The methimazole prohibits the hormones the thyroid secretes from being turned into a form the body can use, which effectively stops the symptoms, but the underlying problem is still there. Add to this a lovely list of symptoms your cat can't tell you is there:
skin rash
itching
abnormal hair loss
upset stomach
vomiting
loss of taste
abnormal sensations (tingling, prickling, burning, tightness, and pulling)
swelling
joint and muscle pain
drowsiness
dizziness
decreased white blood cells
decreased platelet
And it's a perfect storm for an irritable cat.

It doesn't affect every cat this way, and some go for a very long time and do well on it. I've been "lucky" in that my two have both had adverse reactions. Our girl had liver failure. Thankfully, we were able to get her fixed up and do the I-131 treatment that cured her. Our boy has IBD, and the methimazole is making it worse, so he's not keeping weight on even though he's eating more than enough. We're doing the treatment for him in less than 2 weeks. It's expensive, but we figured out that just in the meds alone (not counting the maintenance blood work and any possible issues), it pays for itself in 3 years. Our cats are young enough that they'll almost certainly outlive that, so it's worth it to us to do, and it's made for a happier Isis (our girl) and will hopefully make for a happier Beaker (one of our boys). I'm really hoping it will put an end to the fights between Murphy and Beaker, since Beaker will be less aggressive off the meds. *fingers crossed*
I've said all that to say this. It's very possible that the meds are messing with Scooter in multiple ways, and just made him generally grumpy and resistant to change.