The DDS Compiler v4.0 will not output the correct waveform if NAN (Matlab 'Not A Number') values occur on the Data input. In this situation the DDS output will be a constant value rather than the expected Sin/Cos waveform.
NAN values will sometimes be present in SysGen/SimuLink simulations usually during initialization. An example of when NAN values would be seen is if the Black Box is used and the underlying HDL code has an undefined output state. The undefined output will translate to NAN values in Simulink.
In order to resolve this problem, make sure that the signal connected to the Data input of the DDS is always defined. Either correct the source of the NAN so that NAN values do not occur, or if this is not possible, an enabled register can be used to mask out the NAN values. Many SysGen blocks have valid signals that can be used to drive the enable of a register to conveniently work-around this issue.