chrisjohn -
This sounds like a problem with the drive jumpers.
First of all, there is usually a Primary and Secondary IDE cable - the drives themselves are either configured as 'Master' or 'Slave' on either of those cables (not 'Primary' or 'Secondary'). I assume you're talking about only one IDE ribbon cable (the Primary IDE channel) and either having one or two drives connected to that cable at the same time, right?
The drives themselves need to be jumpered correctly whether they are by themselves or with another drive on the same cable. Since you're having problems with only one drive connected, then it may not be jumpered correctly. It should be jumpered as 'Master' or (on some models, usually Maxtors) 'Master without Slave'. What model drive is it?