I am having same problem too. posted a tread about it a few days ago:
http://duc.avid.com/showthread.php?t=295836
though to add to this thread, I am running PT 9.0.1 with a zed R16 and Win7.
I reinstalled and updated pro tools and now it works. However, just yesterday found one session that is causing the same problem, while others work fine. Interestingly, the session that doesn't work on one computer works fine on another. The other computer is using an mbox 2. Could it be the hardware? The Zed is an asio.
any help please.
Lou