Due to a problem in the Quartus® II software version 12.1 SP1 and earlier, Verilog HDL files generated from schematic block design files (.bdf) may not simulate correctly. This problem occurs when schematic designs contain Altera® primitives. Verilog HDL files generated from schematics refer to these primitives using all upper-case letters. Verilog HDL simulation libraries for these primitives use all lower-case letters. For example, Verilog HDL files generated from schematics may include the module SRFF, while the simulation libraries include the module srff.
To work around this problem, edit any Verilog HDL files created from schematic designs and change references to Altera primitives from all upper-case to all lower-case letters.