If you haven't already, try disconnecting the drives as mentioned above and see if they operate normally. If so, it could be motherboard or software related. If not, the drives may be bad.
If they did seem fine, try with the drives connected but without booting to Windows (say go to the BIOS). If they still seem to function, it's probably some software hogging them. If not, again, probably hardware/motherboard related.
Also, you didn't mention what the machine was. Problems like this are fairly common with older IDE based machines since the drives can both be on one cable/one channel.