This is an old issue with the DVD's of these shows.....the Blurays of TNG, Enterprise and the original series don't suffer from this.
If you set your Automatic 24p output to "off", the dropouts should stop.
It's time for another Deep Space Nine Upscale Project update. I've moved closer to a final workflow for video processing, but have a few snags still to fix. Variable Frame Rate DVDs are basically Satan if your goal is perfect frame delivery.
www.extremetech.com
"Star Trek: The Next Generation,
Deep Space Nine, and
Voyager weren't recorded in anything as sensible as a steady 23.976fps. When these shows aired in the 1980s and 1990s, they were constructed from at least two different types of content: 23.976fps progressive content and 29.97fps interlaced content. Episodes of these shows do not run at one frame rate; they run at different frame rates depending on what's happening on-screen. A show that runs at one frame rate, start to finish, uses Constant Frame Rate encoding (CFR).
Deep Space Nine, TNG, and VOY all use VFR.
Stargate SG-1 and
Babylon 5 do the same thing. Most of the best nerd content of the late 1990s and early 2000s is locked behind media that go for this kind of manipulation."