I remember the "failed to restart player" but was described by empeg as being becuase the player "went off into its own wibbly wobbly world" during the sync.. or something like that. Jiffies sound pretty wibbly to me.
The failed-to-restart-player bug (at least in the case we managed to reproduce) was nothing to do with jiffies. The jiffies thing kills serial input, whereas the player could be brought sharply back from the wibbly-wobbly world thing by sending it a ^C over serial. It's more like there was a subtle (or perhaps unsubtle) pthread_cancel problem; a workaround was applied to the code post-beta11 and will be in the next beta.
Peter