It appears as though Spine 2.0.0+ creates additional folders in the output directory path each consecutive time you export a .json file (which in my iterative workflow, I do a lot).

So this is where my spine file is located:
C:/user/project/assets/scenes/assetname/scene_01/assetname.spine
When I export the first time, a skeleton.json file normally exports successfully in the correct location.

If I still have my scene open, it'll create another project folder in the export path window, like:
C:/Users/user/project/assets/scenes/asset/scene_01/scene_01/skeleton.json
If I export again, it'll look something like:
C:/Users/user/project/assets/scenes/asset/scene_01/scene_01/scene_01/skeleton.json
and so forth...

A coworker has reproduced this issue on a seperate machine using 2.0.02
If I only export once when the file is open, I do not run into this issue.

spine.log:

Spine Launcher 1.8.15-full
Windows 7 x86 6.1
Java 1.7.0-u6-unofficial Oracle Corporation
OpenJDK Server VM
Up to date: 2.0.02
Licensed to: <redacted>
Spine 2.0.02 Professional, LWJGL
NVIDIA Corporation
Quadro 600/PCIe/SSE2
4.4.0
Started.

I should also add this did not happen in version 1.9.17 or before.

1. Open any Spine file.
2. Ctrl+e to export .json file.
3. Observe the exported file's path (ie, "desktop/Spine Issue/skeleton.json")
4. Export again.
5. Observe the exported file's path ("desktop/Spine Issue/Spine Issue/skeleton.json")

image reference of what I'm seeing:
Before exporting .json: http://imgur.com/0gnTbI8
After exporting .json: http://imgur.com/P467sM8 (notice the double "Spine Issue" in the folder path)

I reproduced this by deleting my preference file (C:\Users\myName\Spine\prefs.json), deleting the entire Spine folder, and by creating a new project file from scratch.

Yay!

Great, thanks!