Your posts actually raises five separate issues:
1) If there are oscillations, HydroCAD will generally issue a warning message to alert you to the situation. If you click on the message (in the message window) you will get detailed help on your specific situation. Although I don't know which message you're getting, oscillations can generally be corrected by setting the "Finer Routing" factor to 2 or 3.
2) Also be sure you have defined the pond storage up to some point ABOVE the crest of your weir. Otherwise the software will not be able to accurately determine the storage when these is one inch of head (for example) over the spillway. Again, you should see a warning message if the routing calculation exceeds the defined storage. Click on the message and read the recommended solutions (define more storage!)
3) As for the porous nature of the check-dam, the most accurate solution would be to use a custom outlet device based on actual field tests. A literature search might also provide some useful references, but predicting the exact behavior of your check-dam could be difficult. Perhaps others have run into this??
4) The broad-crested weir procedure in HydroCAD allows the weir coefficient to vary with head, rather than using the fixed coefficient of the basic weir equation. While this may provide greater accuracy in predicting the head-discharge relationship, these (slight) variations often have a minimal effect on the final routing calculations. Before investing much time in determining the BC weir coefficients, I suggest a quick sensitivity analysis to see if this additional complexity is justified. In many cases, a modest change in the weir coefficients will produce only a slight change in the peak elevation, and virtually no change in the peak outflow. Of course, generalizations are dangerous, so do your own evaluation.
5) Finally, unless the 1.5' high check-dam creates a significant amount of storage (i.e. inundates a significant area) it won't have a significant effect on the incoming hydrograph, and may not need to appear in the HydroCAD model at all. A "pond" with no storage will always produce Outflow=Inflow, and its inclusion in the model will only serve to tell you the peak water surface elevation at that point.