I didn't remember having any FMV audio problems when I had last tested out this game, but after stumbling on this thread I decided to go back and check it out.
I tested using the latest buildbot build and did indeed notice the audio problem as well.
In the intro video that plays just after the logos once it reachs the third line of dialoge
"and the rule of the senate elders had begun to fray at the edges" the audio starts cutting in and out.
The problem seems to get worse the longer the FMV runs and on some cutscene videos that are particularly long the audio will cut out and stay out near the end of the video.
As the OP had stated, the audio is only messed up during the FMVs and not during gameplay.
I tried using the "Preset 1 - Safest" settings and also tried messing with the sound plugin and enabling Async, but nothing had an effect.
I tested with older builds and found that they didn't have any issues with the FMV audio so I dug back through the buildbot SVN builds and found...
The last build with working audio was:
pcsx2-5903-windows-x86
With the notes:
"Vsync: Put it back to half slices, there seems to be games which don't like the vsync timing more accurate either way. Until i can work out why we will go back to the old half n half timing which all known games seem happy with."
The build that the audio stuttering first occurs is:
pcsx2-5904-windows-x86
With the notes:
"If you're gonna do a revert, you might as well do it properly If you don't want it doing properly, give it to me."
Not sure what changed between those two builds that caused the audio stuttering but 5904 seems to be the culprit.
I'll post this information to the github in hopes that its useful to the team. I figured I'd post here about it as well incase anyone comes here with a similar issue and is looking for a solution.