Yup. I'm still getting those nice little boxed letter A's on some of my sites since upgrading to OS X Lion. CNet has a very detailed article about the issue.
It turns out that the new sandboxing (which is a safety feature) in WebKit (Safari, Chrome, many more browsers) can't find certain fonts from time to time so it defaults to the last resort option. This last resort font option is a horrible bunch of A's in boxes. Follow the CNet write up by Topher and you should be able to find at least one method for correcting this.