Emulator

Game Name?
Paper Mario: Thousand Year Door

Game ID?
G8ME01

What's the problem? Describe what went wrong in few words.
Punies are randomly disappearing.

What did you expect to happen instead?
Punies to continue following me.

What steps will reproduce the problem?
Any situation where Punies can get "lost", the game deletes them. This includes falling off a ledge, blowing them off a ledge, or across a gap with bubbles. If multiple (20+) are offscreen they become un-rendered and start induced a HUGE frame-rate lag and slowdown in the room until it's left and returned. Returning CAN make them re-appear, but it's still impossible to get all 101 to the end as there's always at least 1 Punie that doesn't come back.

Which versions of Dolphin did you test on?
Dolphin x64 v4.0.2
Dolphin x64 v4.0-707

Does using an older version of Dolphin solve your issue? If yes, which
versions of Dolphin used to work?

The game itself works, but this is my first playthrough via Dolphin in any scenario. 2 different versions both create this problem.

What are your PC specifications? (including, but not limited to: Operating
System, CPU and GPU)
System: Windows 7 x64
CPU: Intel Core i5-4670 @ 3.40GHz (Quad-Core)
GPU: Nvidia Geforce GTX650 @ 1GB GDDR5
RAM: 8GB GDDR2 @ 1866MHz

Are you using the 32 or the 64 bit version of Dolphin?
64-bit

Is there any other relevant information? (e.g. logs, screenshots,
configuration files)
The problem I'm experiencing is accompanied by another issue that people have said was resolved in v4.0-707, which is the loop-frame of the punies being rendered incorrectly resulting in a glitched/garbled graphic.

Backend: Direct3D
Internal Resolution: 2xNative (1280x1056)
Check: Scaled EFB Copy
Check: Per-Pixel Lighting
EFB Copies to RAM
Check: OpenMP Texture Decoder
Check: Fast Depth Calculation