I've just been playing around in 3D in Godot 3.2, and I've noticed on my machine there is a noticeable frameskip every few seconds.
I'm not doing anything complex with my code, just a simple player controller that can move and look around.
This is something unique to my machine, I played it on two other machines and don't notice the frame skip.
Here's an example of what's happening:
https://gfycat.com/blueelegantgonolek
At 2 seconds, and at 9 seconds, there's the frameskip.
I don't believe this is the renderer, I tried changing to GLES2, same thing. I downloaded and compiled the experimental Vulkan 4.0 branch, same frame skip.
Likewise, it doesn't seem to be my scripting code either. I created my player controller in both C# and GDScript, no difference.
This doesn't happen in 2D, I got a semi-complex scene running in 2D and haven't noticed a single skip. This is 3D exclusive problem.
One thing odd to note, whenever the skip occurs, there's a delta time of exactly 0.001388889. Happens every time.

According to the profiler, the Idle Time and the Audio Driver both spike when there's a frame skip. I'm not sure what this tells me.
Idle Time:
Audio Driver:

The reason I ask here is because I have never delved into Godot's source code, I was hoping someone here could point me in the right direction so I'm not going in blind. If there's a better place to ask this let me know.
Let me know if you got an idea of what exactly my problem is. If you need more information, let me know.
My specs:
Windows 10 Pro 64 bit
Intel i7-4790K
32GB RAM
Nvidia GTX 980 TI