Sorry,if you use those settings(hle and audio) you will get some freezes. I don't test games without audio or hle.(unless necessary to get the game to run)
When i put up information on the compatibility list they only apply to the settings I've used, I could add additional information about how it works without sound.
* without hle i doubt you can get freezes, but with it on try using the hammer repeatedly while hitting a tree that releases a switch or some other intensive task.(you get the idea)
HLE doesn't provide speed for Paper Mario and will only cause freezes, therefore it should be disabled. Same with Synchronous audio, it will increase the chances of freezes. In order to test properly, you should use the best settings for each game, otherwise it would be like saying that every game on Daedalus has freezing issues because you're testing with Async (which is known to cause freezes).
@matt: Sounds like a bad dump, you should try using another rom. I personally never gotten a freeze on PJ64. The (E) version won't work well with Daedalus.