I meet all the requirements of FleX (i7 4770K / 980GTX) and I noticed somewhere around version 1029 that I would get stuttering when everything had worked perfectly before. At first I didn't associate it to any one thing, but it was obvious that it happened a lot when I am decapping trash. It also seemed more prevalent early in the game and became less pronounced as I played on.
Once I figured out that it was FleX, I did a little bit of experimenting and found that for me it was liquids that was causing the issue. With just Gibs enabled, I don't have the stuttering I do when both are enabled. Of course I am still playing around. I don't often make Bloats explode, so I'll have to try doing some of that. Mostly I just decap everything and let it stumble around until it drops.
So to the OP, you aren't imagining it, there is something going on with FleX. Whether it's something "broken", or the developer added more detail / complexity / particles / etc, I don't know. If it's the latter, then it may be that none of use will be able to use it with the new system. If it's something that's been "broken" then hopefully TWI can figure out what they've done and undo it.
@ TWI, I was running the game at the highest detail settings @ 1080p. I also have some advanced stuff enabled via the KF2 Tweaker. However these "special" settings worked just fine before the aforementioned issues with FleX. I monitor nearly everything via Afterburner / RTSS / OSD and my VRAM utilization never exceeds 3200MB, so it's not a case of running out of VRAM. The VRAM usage is this high due to some of the tweaks I've applied with the KF2 Tweaker. Again though this was all the same prior to the problem surfacing. When I am not experiencing the problem, my framerate never goes below 100FPS, most of the time it's between 130 - 110. When the stuttering cuts in, I've seen it drop to as low as 19FPS which is quite jarring. Almost feels like ZED time.