Okay, It's not the Pedals and I checked the bottom bracket and it all seems to be fine. I did compare the old chain to the new and the only difference is that the old chain was a Shimano HG73 9spd chain and the new chain was a Shimano HG93 9spd chain. I thought that one 9 speed chain is the same as any 9 speed chain as far as size and fit go. Is there a big enough difference between these two chains that it is the problem?