The problem will most probably be the Adobe Reader Plugin that doesn't work with the newest Safari version anymore (as confirmed on Adobe's web-site). The Shubert Plugin is not free of problems and not necessary, for Safari still has its own plugin for viewing PDFs!
So here's my solution:
Delete the AdobeReader Plugin from the Internet Plugins folder.
Delete the Shubert Plugin as well.
Open the file com.apple.Safari.plist in User/Library/Preferences folder (you can do it with X-Code, but also with applications like Prefsetter)
Find the setting "WebKitOmitPDFSupport" an set the Value on "NO".
Save the file.
Now you should be able to view PDFs directly in Safari again, without unnecessary downloads and much quicker than with Adobe Plugin!
Hope this helps.