Because the custom chef run happens first before integration, the custom chef will always fail on newly booted instances.
The dependency is here: https://github.com/engineyard/ey-cloud-recipes/blob/master/cookbooks/thinking-sphinx-3/recipes/thinking_sphinx.rb#L61
Current workaround: Deploy, then re-run chef.
Sequence:
Boot
Main chef run succeeds
Custom chef run fails
Integration is not triggered
Deploy
Click Apply on the instance
Main chef run succeeds
Custom chef run succeeds