Not to steal this thread, but I'm also having similar issues.
A number of things stopped working from doing this. Jetpacks Share icons dissapeared. My Theme (Shiword) slideshow on the front page stopped working. Facebook Connect and Facebook activity widget. The connect stopped working altogether and started reloading reloading reloading. Pages wouldn't stop loading, and if you tried to login via FB then it would auto log you out. The activity widget only displays on 50% of pages, and seems to be on random posts/pages.
I tried putting all JS back into the header, but it didn't solve the problem, then I put it in "Un-Blocking" header, but didn't fix anything either.
Would love an in depth tutorial/info on this plugin, because it seems simple things that should work end up having disastrous effects and screwing with a "Finished Website". I say finished, because I heard this was bad to install if you haven't finished messing with your theme, plugins etc.
So I put it off for about 3 weeks until I was sure I was done.