I've found that Handbrake 0.9.4 often will not load up a re-muxed file containing a newly converted or altered soundtrack. It just crashes the main CLI process in Windows or says it cannot find a valid file in OSX. I've read of a lot of other people running into a similar problem with certain Blu-Ray movies and what not. I think they traced the problem to ffmpeg, but even though this issue was known in SVN builds prior to the release of 0.9.4, it was NOT fixed for 0.9.4. The odd thing is that 0.9.3 works perfectly fine with such files. I've had to use it a few times in the past few days with DTS conversions, which died in 0.9.4 but worked fine in 0.9.3. I'm glad I kept it around since they only maintain source versions of older versions of Handbrake on their site for some reason when this shows it would be a good idea to keep older binary versions around if their new versions are so obviously buggered (i.e. they knew it wasn't fixed in 0.9.4 and released it anyway, removing the older version where it worked and have had no official non-SVN updates since then).
Try the nightlies -- there have been a ton of changes that improved encoding from HDDVD/Bluray sources.
You should be used to the long "official" release window of the Handbrake project by now. Since .9.4, there have been a number of developer snapshots (one very shortly after to fix the problem you're likely referring to), and now they make nightly builds available. IMO, the significant changes and improvements made in the six months since .9.4 was released far outweigh any potential instability you might encounter (although unlikely in my experience).