I have this sorted I identified that there was a discrepancy between the plugins of the manually exported plugins in eclipse against the plugins that were being downloaded from the Juno repository using the maven tycho download.
The org.w3c.dom.smil version 1.0.1 was being downloaded which had a missing dependency. While the manual export which was using the running platform target platform(Kerpler) was version 1.0.0.
I discovered this by doing a diff on the plugins directory of both files.
To get around this I created a tycho target platform file and used this as my target for my build instead of the repository.