Hello, drjasonclark:
As previously mentioned, the appleeventsd issue is a Mac OSX 8.2 issue, and as such, you are likely to have the same issues in any version of EndNote, not just X6. Please contact Apple to regarding getting the issue permanently resolved. http://www.apple.com/feedback/macosx.html
However, most people experiencing this issue are reporting slowness using the EndNote program and errors in Word, though, not difficulties online searching, so I want to make sure that your searching issues are in fact caused by the appleeventsd issue. If not, we should troubleshoot to see if we can find a permanent resolution for you. Does ending the appleeventsd task in Activity Monitor correct the searching issue, even temporarily? If not, your problems are rooted elsewhere and I recommend contacting our Technical Support directly by phone or email to look for a resolution. http://endnote.com/support/contact-support