First, make sure that your drives are using DMA. This can be checked by going into your Device Manager, expanding Ide Controllers, and checking the advanced properties of all your IDE channels. Make sure the transfer mode is on 'DMA if available'.
Other than this all i can think of is that there is a program in the background hogging your drive when u first put a cd in. However since u have just done a fresh install, this is unlikely. (the fact that both drives do it points to the fact that its not a problem with the actual drive, and you will probably have the problem whether you get a new one or not)