Just to be clear, these are two drives inside your computer, connected directly to your motherboard?
What's happening is that Vista assumes that both drives are removable, which is true to a certain extent because SATA ports are designed for drive hot-swapping. Go to Device Manager (type in "Device Manager" in your Start menu search box then press enter). Look under Disk Drives and you'll see both your drives listed.
For each drive:
Right-click on the name and select Properties
Go to the Policies tab
Make sure the drive is set for Performance, not for Quick Removal
This should tell windows to not list the drives as being ready to safely remove. Good luck!