When the diagnostics for a SQL_GROUP_LIST loader job runs, part of the check is to get the number of groups returned by the query in the Group query parameter. If the SQL call fails, it appends the failure to the accumulated report in progress, sets an isFatal flag, and skips most of the other checks. One check that isn't skipped is the "see if the groups like count is similar to the number of groups returned" check, which compares the number of groups already in Grouper versus the query results. However, the query results are null, resulting in an uncaught exception. Since it's uncaught, it loses the accumulated report results up to that point, including the diagnostics error reporting that the group query failed.
The only feedback the user sees is "Error: Problem calling method loaderDiagnosticsRun on edu.internet2.middleware.grouper.grouperUi.serviceLogic.UiV2GrouperLoader". This is also the only thing that gets logged. This makes it hard to pinpoint that the problem was the groups query, except by trial and error.