CDN on Multisite: Source File Not Found errors

In the last few updates since 0.9.1.3, I’ve been having a new issue with push CDN with Cloudfront. I’m running WP as multisite with subfolders (3 sites total).

On my site in the domain root, everything seems to be working normally, but on both my subfolder sites I’m getting Unsuccessful File Transfer Queue warnings. If I empty/delete the queues the warnings come back quickly with Source File Not Found errors.

It’s particularly noticeable with the wp-includes folder.

As an example line in the Unsuccessful Upload Queue:

Local address:
/[localrootaddress]/[subfoldername]/wp-includes/js/wp-lists.dev.js

Remote address:
[subfoldername]/wp-includes/js/wp-lists.dev.js.gzip

Error:
Source file not found.

Is there something I need to alter in my configuration, or is it something in the plugin itself? Should it be looking for wp-includes under the subfolder name or directly under the root domain?