The issue was caused by missing relations between smoke domain and flow/source objects. This happened because smoke's modifier only iterated base objects and ignored cases when flow/source could be linked to scene via dupli-group and does not have real base. The same seems to be still needed for fluid and dynamic paint modifiers, will do it as a separate commit. Reviewers: campbellbarton Differential Revision: https://developer.blender.org/D1172