Smart Compilation feature of quartus.exe/quartus_sh.exe never was 100% robust, but in v. 9.0 it works better than in the past.
Now came v.9.1 and all of the sudden smart compilation is more fragile than ever.
I use a new version just for a couple of week and already found two unrelated project assignments that completely break smart compilation:
1.
set_global_assignment -name FLOW_ENABLE_TIMING_CONSTRAINT_CHECK ON
2.
set_global_assignment -name EDA_SIMULATION_TOOL "ModelSim-Altera (VHDL)"
In the later case, I guess, any other option that cause quartus_eda to run during compilation will lead to the same result.
Now, thinking about it, my first case causes quartus_tan to run twice.
Could it be that every additional step in standard (_map->_fit->[_cdb]->_asm->{_tan ot _sta}) compilation routine breaks the Q9.1 fragile smarts?
