When creating a new Checklist custom field, the Checklist Searcher will be setup as the default Search Template. However, if you have installed a previous version of Checklist, it is possible that the custom field has no associated search template. If this is the case, to make the checklist searchable, Edit the checklist custom field and change the Search Template to the Checklist Searcher.
It is very important to re-index JIRA if you want previously created checklists to be searchable.