At the time of this post I can't replicate that issue. The Close button generated by lightbox is a link with href=#, which could cause SoftScroll to cancel the link's default action. Fortunately SoftScroll allows # links to be excluded by adding a class to them, so you should be able to hack lightbox as follows:
In lightbox.js find this line:
and below it add:
objBottomNavCloseLink.className = 'noSoftScroll';
Where used, return should be executed unconditionally and always as the last statement in the function.
That's my signature, it's not part of the damn post!