As to the issue with parenting in blender. You have to reset your objects origins and make them all have a 0 offset to the parent. Shift+c to reset 3d cursor to scene origin (0,0,0). Select the parent -> Object -> Transform ->Origin to 3d Cursor. Then with the parent still selected-> Shift + g -> Children (to select all children objects). Alt+p -> Clear parent and keep transform (to clear the "wrong" parent relationship), then keeping all the children selected Object -> Transform -> Origin to 3d Cursor. Then with the children still selected, shift select the parent, ctrl + p -> Object (to reparent them).
Do not parent glass and/or other transparent objects to the main parent. Also if using different effects on different objects, those with the different effect cannot be parented to the main parent (they will have their effect overwritten by the parent's)
Doing the above avoids the issue with objects being incorrectly moved and/or rotated by the exporter after being parented since it resets the transform matrix of all of the now parented objects.