On a hunch I opened up an affected project as a folder (as opposed to a workspace containing the project folder), and files were scanned. Whatever the underlying cause is, it appears that the workspaces feature is a trigger for this. Perhaps files are referenced differently in this scenario, resulting in the lack of support for UNC and remote paths described over on Github to become an issue.
"name": "IDAM API",
"name": "IDAM GUI",
The API folder contains the Laravel 5 project (standard skeleton, tad messy as libraries were merged into the same repo).