Cracking is due either to material problem (check residuals and/or stringers) or having the material get too cold during/after quenching.
You need to keep the temperature of the material above 300F (preferably 400F) before quenching. This is easy to check these days with a infrared non-contact thermometer (in the old days, you had to use tempil-sticks). Your actual maximum quench exit temperature will have to be determined by trial and error, but I'd guess around 450F. You may find that quench exit at 500F is fine as long as it cools below 350 before temper.
Which makes me think, your flattening fixtures are just heavy pattens, right? Maybe you need to preheat them to 350F to keep them from quenching your blanks to below 300 before the tempering furnace can get the temp high enough to prevent cracking.
rp