It may be the heat bending the balsa as much as the Monokote tugging on it.
I never Monokote flaps, just prime, sand and paint. My thinking is that makes them stiffer. And I'll probably dope some carbon veil on the flaps for the wing I'm building now, hopefully adding more stiffness. I've never been a fan of Monokoting any solid surface, only my wings. I have 'koted a stab, but don't recall it fighting me like you're getting.
Rusty