Hello again everyone. Sorry I've been away. I've been working on Spriter 2 related things, but I will fix the spritesheet issues. I filed a bug as per 
Ashley 's suggestion, and it should be simple to update the plugin once the SDK supports animations.
I made an attempt to circumvent the issue using images instead of animations under the hood, and it doesn't seem like there'll be an easy way to do it without breaking projects and redoing a lot of work on the plugin.
Thanks for your patience again everyone.
Hey Lucid, thank you so much for your work on Spriter!
I just wanted to let you know that the issue of having spriter objects showing the wrong image when you have more than one scon in the project is due to the way C3 bundles sprites into a spritesheet. And therefore with Spriter, we are essentially adding the spritesheets into a bigger sprite sheet without updating the json information in the scon file to account for that.
I don't know if an easy solution would be to set the spriter objects as tiled sprites rather than sprites? Tiled sprites get their own spritesheet, and so that would avoid this issue.
Either way - good luck, and many thanks for reviewing the issue!