ruby-runtime 0.13 seems to be causing an issue where the configuration for projects is getting tagged as Old Data and, as a result, skipped from being read and used. This, in turn, causes issues with plugins like rbenv from being able to be persistently configured. The config.yml is properly written and runtime changes work, but are lost on restart. This seems to be presumably because of the data being flagged as old data.

Rolling back ruby-runtime to 0.12 resolves the issue.