I think I have an answer for this.
I experienced multiple entries on my SD card quite a few times, tried formatting, secure deleting all free space with specialised programs (they took hours writing 0's multiple times over and over) but nothing worked. Then my phone had a restart issue, (kept restarting every few minutes) so i sent it off for repair.
I kept my SD card and didn't touch it. When my phone was returned, I put my SD card back into the phone (unedited) - whereas before it duplicate entries and now suddenly all seems fine. I have no duplicate entries at all.
When my phone was returned to me, they had reset it, and I had to go through the process of setting it up again as if it was brand new. My contact and everything were downloaded, so I hadn't lost anything.
I think the problem is that the phone creates a database of the music on it and saves it on the phone, so it is not the SD card that has the problem, but the phone. For some reason there is no way to properly wipe the phones database other than doing a hard factory reset.
I haven't tried it again yet myself because I have no duplicate entries, and I don't want to test it. Anyway I am convinced it works. The steps are as follows.
1. Remove SD card and SIM card.
2. Go to Settings > About > 'Reset Your Phone'
3. Follow the on screen instructions
4. When it comes time to set up your phone again, put your SD card and SIM in again
The duplicate entries should be removed.