I just noticed that building an existing static resource change the MIME Type. I've only tested with CSS files, but when I build a static resource of type CSS, it keeps the same content, but changes the file type to application/octet-stream. This stops VF pages from accessing that CSS.
The files in the local folder stay as CSS files, but in Salesforce the file type changes.
Let me know if there's any more info I can provide.