The next thing to look at is how the drive is connected to the computer, If you are using IDE drives make sure that you don’t have the drive slaved to anything or have anything slaved from it. The drive must be on its own IDE buss set as a master.
The only way I can connect my second (samples) hard drive is to slave it to my existing drive (the new drive is 7200rpm and has 8Mb cache).
I can't do anything about this and I know it's not ideal but will there be any issues I might encounter by doing it this way?
At worst you want to make your sample drive the master and a CD/DVD drive the slave. Making a second hard drive the slave will be slow and risky. The signals in the middle of the cable tend to have reflections and are more susceptible to noise.
You should be able to find a PCI IDE card for under $30. Install one and put all of your hard drives on their own cables.