The multibranch indexer does not traverse sub-folders in subversion branches, if their revision is older than the parent directory.
Given this folder structure in the trunk:
Branching projects into tags/1.0/projects yields
Note that r4 is only applied to the new folders, and the branched folders retain their original revision (because they haven't changed).
The expected behaviour here (and surely, the purpose of the multi-branch system), is for it to automatically detect the new branch and generate jobs from its Jenkinsfiles.
The branch indexer should be able to work out that the 1.0/ folder didn't exist before, and index everything inside it at least once regardless of its revision.