Well I don't think there is any standard for floppies, it can be one way or the other.
check the board connectors also, not just the drive connectors.
As for the cd-rom, make sure the jumper on it is set to the right position. (along with the hdd because if you have your cd-rom as a slave and a hdd as a master on the same controller, sometimes the hdd has to be set to "master with slave" instead of just "master")