Hi,
Its been a while since my last post, but I have finally solved this problem. It seemed that even if the drivers where part of the driver packs they where not installing. The problem seemed to occur on many different computers including laptops, so after spending many many weeks looking in to the issue, I looked at DPINST.exe.
It seems that Microsoft has two switches that allow you to automate DPINST to not show its screen to the user. You can either use <quietMode/> or <suppressWizard/>. Now both do exactly the same thing, except if you use <quietMode/> with <legacyMode/> it will not install some drivers, even signed drivers. However if you use <suppressWizard/> with <legacyMode/> it workes all the time as you would expect. There is no information on the Microsoft site about this issue.
http://msdn.microsoft.com/en-us/library/ff553383.aspx
After knowing the answer and searching on the interent I realised others have the same issue, so here is the solution.