Even with the big ol' timothy/orchard grass 100lb bales I was used to in Washington state, two flakes twice a day wouldn't be nearly enough for a normal TB, let alone a skinny one. Up the hay. If he colics if he gets too much at once, then just split it up. Two flakes THREE times a day, rather than two. And double the beet pulp while you're at it.
Can't guarantee your guy doesn't have other problems (bad teeth can result in colic, btw, get a vet out to check for medical issues) but my little QH would be losing weight given what your guy is, so no wonder a TB isn't doing well on it.