The countersinks on a bce chassis are not as deep as the stock chassis. You can countersink them a little deeper and they will work fine. I run the BCE chassis on my mugen and this has worked quite well. If they don't seat well on the stock chassis I would imagine that they were over tightened. When they are wrenched down hard it makes the plastic deform like a play dough fun factory. Be carefull not to over do it and its best to do it by hand and not use a power driver.
Are the plates XD or Gen 2? The XD plates were created to help fix many of these kinds of problems. They have been a huge improvement.