There's probably a couple reasons for this.

1) Your system is running in Cable Select Mode. Meaning that it picks the first hard drive on the ribbon and assumes that is the master drive.

2) Jumper is set incorrectly. The jumper is probably set to either CS (Cable Select) or MA (Master) it should be set to SL (Slave) and your main hard drive should be set to MA (Master). This is the most probably reason as to why it's happening.

3) I've had problems with hard drives that just don't want to work when other drives are on the same ribbon. I don't know why it is, I don't know what makes it that way, but I had a Western Digital that would only work in CS (Cable Select) and if another hard drive was installed, no matter where on the ribbon it was, it wouldn't work.

You can buy just a case for an external hard drive. I think they're like $30. You can drop any hard drive into it and it'll act as an external drive. Simple and quick fix if you want to keep it external.