When things don't work out the way you expected them too (and they won't), a great tool to use to help track down the problem is the "Test" button. This button renders the i-statements that any given SoundObject will generate, and it comes in very useful with PolyObjects. So, if you've got a PolyObject that won't render when you Test it, drill down into it and test its constituent notes, Testing and drilling down into its sub-PolyObjects as well. You'll eventually find the cause. Examine NoteProcessors and the Time Behaviors of each SoundObject; these can be common culprits with sound problems too.

If one follows the best practice "Group co-reliant notes together into PolyObjects," this also makes it easier to debug problems. You can isolate PolyObjects in the main score easily by soloing that SoundLayer, etc. (since they won't rely on other SoundObjects for their sound) and investigate the problem that way; many times, you'll find that the problem stems from the PolyObject not being as independent as you'd thought.