Well its been quite hard to diagnose the problem. If you do a search on these forums you will come across various threads detailing the problems I have been having, at first I thought it was bad ram, as all my disk utility was saying my drive was fine. Then I tried the TechTool Pro and and it reported I had 2 bad blocks, which, correct me if Im wrong, can cause problems if those blocks are located where the disk needs to access important system files...
2 Bad blocks found
Surface Scan <Failed! (-4)>
So after seeing this I am preparing to buy a new drive, but first, as I said before I will try a zero and reinstall to see if this helps. I havent had the time to do this as its such a big job, hopefully I will perform it in the next couple of weeks, unfortunately I did not keep the installers to lots of my programs so I will have to sort this out in the meantime!