TommyGirl,
Technically insurance company are correct - AIB have an interest in the policy and therefore cheque has to be made out to them, however, common sense should prevail here, as you outline, you've had flood damage which presumably cheque is designed to cover (along with accommodation costs) - if AIB hold on to the proceeds, you can't fix up house - therefore their security (your home) is not being maintained properly. They do have the right to insist that monies are being spent on repairs (which is what you want to do anyway).
Seek to speak with your local manager - urgently.
pjmn