I will have a look but I think in the scene tab you choose which layers get exported right?
Yep, it's the first thing I've checked, only first layers renders.
From my testing it is this layer selector that affects which objects are exported.
Yes, and I found problem, for example if in my other scene instanced objects are on 1, 5 and 10 layers then in the main scene those 1, 5 and 10 layers must be active to.
I tried v-ray for blender and renderman exporters and they solve this some how, layers dont bothers them if some objects are assigned to group they renders, no mater what layers are active.