Ashley
I have installed C2 R172 today and the bug came back. You are right , its not about the runtime.js UTF8 with or without BOM.
The bug is in common.js. I just do this.
1)Copy common.js to desktop (since you cannot edit and save in Program Files)
2)Open common.js in Notepad++
3)Press spacebar in the editor
4)Save
5)Copy and replace back to webstorage plugin folder.
I've tested in CocoonJS Launcher v2.0.1 via preview with empty project+webstorage and the solution works. Strange right ?
The file is actually just empty file (with space). I've attached the file if you want to test.
https://dl.dropboxusercontent.com/u/65841566/common.zip