Richard Huxton provided the answer: It's a prepared query-plan, which means it can't plan to use the index because the next EXECUTE might have reconciled=true.

Bryce Nesbitt wrote:
...Which is all good.  But the Hibernate version of query still takes several seconds, and still appears in my pg_log slow query log:

LOG:  duration: 2248.662 ms  statement: EXECUTE C_51443  [PREPARE:  select count(vehicleeve0_.VEHICLE_EVENT_ID) as x0_0_ from EG_VEHICLE_EVENT vehicleeve0_ where (vehicleeve0_.CSO_ID=$1 )and(vehicleeve0_.RECONCILED=$2 )]