Well....I started comparing plugins on my virtual machine etc. Then after a brief coversation with a developer and some use of firebug, the issues was solved!
Looking at the css for the for the lightbox the prevlink and nextlink divs (line 57) have been given a width of 49%. When testing with firebug, the nextlink div was being pushed down below the other one.
I changed this value to 40% (just to make sure) and the lightbox is working as expected. I understand that there is now dead space in the middle of the image but that deosn't really concern me too much.
Still a little odd, but anyway.
I have also tweaked the z-index of some of the div. This is because I have a the sliding panel plugin installed as well.
The lighbox is actually loaded into the footer of the page, is ther a way to get it to be loaded into the header?