Clock uncertainty warnings under 10.0

I have a project that works fine under 9.0 - no timing violations. I upgraded to 10.0 and rebuilt without any warnings. If I now go into TimeQuest and perform a derive_clock_uncertainty followed by an update_timing_netlist, and then write out the .sdc, the new .sdc appears to be incomplete. When I build with the new .sdc, Quartus issues critical warnings that no clock uncertainty assignments exist for several of the signals. A search of the .sdc shows the signals in question don't have set_clock_uncertainty for the path in question, although the .sdc does have uncertainties for many of the paths and has all of the expected sections. Is there an additional step that's now needed? I've tried using the -overwrite option on the derive_clock_uncertainty but (as expected) that doesn't change if an uncertainty assignment gets created.