This change can potentially affect existing solutions (eg. saved replays). When a lemming explodes, the game waits a specific number of frames before actually removing the lemming from the level. Depending on how Lemmix is programmed, it's quite likely that when you change PARTICLE_FRAMECOUNT, you are also increasing that number of frames by 1, thereby delaying when the lemming is actually removed. This in turn can affect the timing of nuking--when player starts nuke, the game starts the countdown lemming by lemming, frame by frame. If a lemming is in a state where it's not already removed but also not eligible to start a countdown (eg. it is already splatting, already has a countdown due to assigned bomber earlier, or it is already exploding but not yet actually removed, etc.), the game doesn't move on immediately to the next lemming to assign nuke-induced countdown, it still waits for next frame to move on to the next lemming. As a result, changing how long after an explosion before the lemming is removed from level can, in a suitably arranged situation, slightly affect how soon the next lemming after it gets its nuke-induced explosion countdown started.
It's true that most solutions will not utilize nuking in frame-precise manners so the overall impact will be quite low, but it is still a change that can in principle affect emulation accuracy in a way that impacts viability of level solutions, and therefore not an acceptable fix for any official LemmixPlayer versions.
I'd suggest looking for a different fix that does not require changing PARTICLE_FRAMECOUNT etc. In fact, given what I said above, I'd venture a guess that maybe the bug is a side effect of the lemming also getting removed right at the end of completing all its frames for the explosion particles. Perhaps the lemming got marked as removed, and as a direct side effect then the work needed to make the final rendering happen right away (ie. without requiring scrolling the level) was unintendedly skipped, leading to the effect you observe.