You didn't say what you've done or if they were SATA drives but I'm guessing you're using your old IDE drives. I hope you did a back up of your important data and software preferences before you started.
Could be some BIOS settings, there's usually a 'safe default' menu item you can use to automatically configure the basic safe settings to get up and running.
I don't know your level of knowledge, so if these are your old IDE drives, you'll need to make sure the master/slave jumpers are correct for your new buss, pick one of the drives for the OS, reformat, and do a clean install of the OS on the new machine. Once running you can install the second drive (where you saved all your data) and it should be seen by the OS.
It's really hard to say without knowing what you've done/are doing, so this is just the basics. There are lots of places to go wrong. After re-reading your post, I suspect the BIOS settings, see if you can find that safe default option.
GL