So, I think there's a bit of a math error in Particular (even in Particular 3). Even when all the clips in your main clip are exactly the same length and the exact same framerate, I've discovered that there are still blips. Turns out that if you have a clips that are 5 seconds long, for example, to produce clean cuts for each clip in a group of particles, there needs to be some lead time after your video is over. One frame per clip, to be precise. I had to deal with a video file comprised of 74 5-second clips and have no blips in any of them after I did this:
Create a composition that's the length of all the clips together.
Make all the clips short by one frame (0:00;00 to 0;04;29, so the next one starts at 0;05;00).
Arrange the of the clips (using the Sequence Layers in AE, for example) so that they follow one after the other.
Then, add to the composition in frames the number of clips you have to the END of the video. You can make it black video, blank, some other randomness, doesn't matter.
So, for 74 150-frame clips (five-second clips in 30fps) video, I created a composition that was 11100 frames long (06;10;10)
Made each clip 149 frames long,
Arranged the clips sequentially,
Then added 74 frames of nothing to the end (making the comp 11174 frames, or 06;12;14)
The garbage frames at the end aren't shown, and all the clips should run normally.
I'm posting this for others who may have issues with this (including me in the future). I'm sure the OP probably figured it out by now (it has been almost 10 years).