I checked and didn't find the same scenario like mine (albeit similar out there).
I have a Roku Express. Whenever I am on Amazon Prime I have an audio synch issue that appears to be unrelated to my hardware. It only happens with Amazon Prime (Netflix, YouTube, and MLBtv work just fine). What happens is whatever show or movie I am watching will randomly de-synch and be misaligned by a few seconds. Here's where it gets even more odd. I can watch a show with the audio a couple of seconds behind, but as soon as it goes to commercial, the commercial's audio is perfectly synched. Then, when it goes back to the show, the audio is back to not being synched correctly. It should be no surprise then that commercials have perfect playback, but videos have buffering issues.
Here's what I think is going on. I think Amazon's content servers are not communicating very well with Roku's servers, and I think it might be intentional on Amazon's part to get people to buy their Fire Stick. It could be that the commercials are on a different server set up to have flawless delivery to Roku (after all, advertisers would not accept substandard delivery for the prices they pay), and the content is on another server that gives lower priority to Roku than Fire Stick.
Curious what your thoughts are and if you know a fix (if a fix exists, then I would be wrong, and I'd happily be wrong to have a fix that doesn't require me buying a Fire Stick).