As of 2 days ago I am getting misleading results in doing custom field search. My team has a Salesforce ID field where we cross reference CRM cases and we have always been able to search through the field using global search or writing an advanced query with the ~ operator. It doesn't seem to quite work now. I have two JIRA cases with the same Salesforce ID, and it is only returning the first (numerically and chronologically) and not all of them. The text box is configured with the free text search template.
I have also re-indexed the instance as well.