From a jira-user post:

I also have 3.0 running successfully, but I am getting the same "Check
SearchRequest for Relation 'ParentProject'" issue.

I created a filter which filters on a custom field. When have the Integrity
Checker cleanup the issues above I notice my filters (only the ones
filtering on custom fields) get removed. Also noticed when I create
statistics portlet based on the filter using the custom field, the
statistics show up fine, but if I click one of the links in the statistics
portlet I get an odd error message (don't have it handy right now).
Statistic portlets based on standard JIRA fields work fine.