That conflicts with my understanding of "custom objects".
With c++ "object arx", you can write definitions for custom objects.
Lots of programmers do this, not just Autodesk.
The Mapcad guys did this for their nice tools.
Anyway, these custom objects get handled in two ways:
1) if the full C++ prog, or the object enabler for the prog, are loaded, the object is displayed using that program's logic, and the entities will list as "AEC_Points", "Mapcad Leader" and so on, their correct names.
2) If the prog or OE is not loaded, the items display as "Proxy_Objects", and Autocad shows them using their default linework display. So if an AEC_Contour was derived from a polyline, Acad shows the item like a pline.
So to say that saving in vanilla acad 2010 will save the items as proxy objects, does not make sense.
When you open the items back in C3D, they will not be proxy objects but aec_points or whatever.
It very well may be that saving in acad 2010 does save the objects in a state where they have less data, thus a file size reduction. This would be the same as an object's style having an effect on the file size. I would have to test to see.
I still see confusion on the OP issue though. You must run some basic tests to narrow down why files would jump around in size.
I always tell people to watch for excess app ids, but I guess they are not the issue as they are hard to get rid of. You would see a jump up, not up and down.