One of my colleagues pointed out to me that the new Matlab R2014 changes its compiling behavior, and instead we should use a slightly different compiling command now:

===Old===
$(MATLAB_DIR)/bin/mex $(MAT$(PROJECT)_SRC) $(STATIC_NAME)
CXXFLAGS="$$CXXFLAGS $(CXXFLAGS) $(WARNINGS)"
CXXLIBS="$$CXXLIBS $(LDFLAGS)"
-o $(MAT$(PROJECT)_SO)

===New===
$(MATLAB_DIR)/bin/mex $(MAT$(PROJECT)_SRC) $(STATIC_NAME)
CXXFLAGS="$$CXXFLAGS $(CXXFLAGS) $(WARNINGS)"
$(LDFLAGS)
-output $(MAT$(PROJECT)_SO)

Not sure if the new command will be compatible with older versions though, but I think it'll be worth noting here for the record, in case someone bumps into the same problem.