Bagels

I have been successfully baking bread for years but I have recently been attempting to make bagels using Peter Reinhart's recipe and also his whole wheat bagel recipe.  With both types the bagels either lose loft in the boiling stage or flatten after baking.  I use good ingredients and mill my own flour for the whole wheat version. 
What are the likely problems.  Do I need to force more flour to make an extremely stiff dough?  Help, I live in a lox/bagel/corned beef wasteland.