[ddouglass]

No you do not need .BIN files in with the KMA files. For the Remove Silence Hoster only looks at the KMA files anyway so the .BIN files are not hurting anything being there.
Is the Remove Silence always stopping at the same point? In other words seince the first error, is it hanging now on the first song it is trying to process?
If this is the case, then open the Edit Songs Tool, select the No S-E button, then put a "*" in the Search box. Click Find. The first Song in the list is the problem file. Note what it is (Brand, DiskID, BookID etc) so you can re-import it, then delete it. Try running the Remove Silence again to see if it goes on.
I have also found that it won't work on any Audio files that you have imported because there is no video with it for it to set in sync with the audio.