Recently, when running Safari's Universal version on my Intel Mac, I was not able to see any Flash content. I would get a blank screen or window with a Quicktime Q and a ? in the middle of it. Viewing Flash was fine using Safari under Rosetta, but then page loads and navagation weren't as snappy.
I couldn't believe it was QuickTime, because QuickTime itself is also Universal. It was driving me crazy, because not everyone was having the same problem, but I finally discovered the fix. It has to do with how the MIME settings are configured. Apparently, configuring QuickTime to play Flash confuses it into trying to use the PowerPC version.
The solution:
Mac OS X Hints
http://hints.macworld.com/article.php?story=20060223002831909