Input monitoring is indeed broken in 10.3.9 Sometimes it works, usually it doesn't. It's most flakey when the input of the track you're trying to record to is set to a bus. So it's a real pain when you're trying to bounce down some processed tracks.
I'm using Mavericks, but as soon as I managed to downgrade to 10.3.8, it worked flawlessly, so clearly something broke between the two versions.
I also had the error of the Pro Tools logo just flashing for a second before disappearing after trying to uninstall 10.3.9 and then install 10.3.8. So I followed these instructions very carefully (they're halfway down the page):
http://duc.avid.com/showthread.php?t=350337
You should note that in order to delete some of these files, you have to "show hidden files":
http://ianlunn.co.uk/articles/quickl...s-x-mavericks/
Also, in the instructions above, there is a small error:
com.digidesign.ProTools.plist
DigiSetup.OSX
Pro Tools Prefs
Are in ~/username/Library/Preferences, NOT ~/Library/Preferences