simon, this could be some of two things
firstly if the 2 sata discs have been uses previously by yourself or someone they could have been setup and running in a raid setup (this means the two discs appear as one and when a piece of data is written to them the data is split across the two hdd's. (hard to tell fully from your description if this is the situation, i suspect not though)
the second is that you have two brand new sata hdd's and your installing them, firstly look on the hdd's and check the jumpers are set to cable select then i would check the issue isn't that the hdd's don't have have any partitions or formatting.
download something like UBCD4 (ultimate boot CD 4) boot into the environment and use the hdd tools in there.. UNPLUG the working hdd before this.
use the tools to create partitions and format the discs.
hope this can help.