Hello, I have the same or very similar problem with a Captivate 9 software recording as described here: https://forums.adobe.com/message/6173519#6173519.
Since this thread is several years old, I have opened a new one.
The hiccup/stutter is especially noticeable with many short slides in succession, in which “audible” audio is played as the slide transitions. If only the CC button from the player is removed, the problem persists. If I uncheck on each slide the box for slide annotations to be displayed as CCs, the hiccups are gone. The problem occurs in different browsers on different PCs. In HTML5 it is quite conspicuous while it is barely noticeable in Flash. The problem can be avoided by leaving adequate audio pauses at slide start and end, however this is hardly feasible with multiple very short slides.
It also reminds me of the problem that mouse clicks at the end of slides make the audio “hiccup”, if it is audible at slide transitions (https://forums.adobe.com/message/8761850#8761850). This seems however to be a separate issue, since my problem occurs also on slide transitions without mouse clicks.
Best
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