I think the problem is that two of the modules have their files under "src" rather than "resources". This may have worked previously, but there was a change recently to be more consistent where we look for files. Note, that in that in a file-based modules where all the files are static resources, the resource directory can be flattened out. I'd probably recommend leaving it for consistency anyway.

see
https://www.labkey.org/wiki/home/Documentation/page.view?name=moduleDirectoryStructures