Thanks for your input again Loosecannon.
What I am trying to say is With the titles, photographs, Video files - which is the start of every wedding I produce - If it is all made on my hdd everything works as it should.
When I make the same project on my extra ssd everything goes awry. Even if I leave the video files on my hdd and import them on to my ssd to work on or if I import them direct to my ssd from the sd card the outcome is still the same.
I wonder if I should try putting the aux files on to a different drive than the ssd to see if that is causing the problem. As you say I don't think studio is causing the problem.
I think it is something to do with my new Samsung 840 pro drive I have put in.
Maybe it is because my motherboard is only sata 2 and perhaps it needs sata 3. But replacing a motherboard seems a bit extreme just to find out. If it is due to my motherboard, I believe I could purchase a sata2 to sata3 converter card and try that first.
Apart from that I can't think of anything else to try only to take the ssd out and jump on it.