diff --git a/audit/src/org/labkey/audit/AuditLogImpl.java b/audit/src/org/labkey/audit/AuditLogImpl.java
index ac0364a9be8..9c7e82bea13 100644
--- a/audit/src/org/labkey/audit/AuditLogImpl.java
+++ b/audit/src/org/labkey/audit/AuditLogImpl.java
@@ -56,12 +56,13 @@
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.LinkedList;
 import java.util.List;
 import java.util.Map;
 import java.util.Queue;
+import java.util.Set;
 import java.util.concurrent.atomic.AtomicBoolean;
-import java.util.stream.Collectors;
 
 public class AuditLogImpl implements AuditLogService, StartupListener
 {
@@ -248,7 +249,7 @@ public ActionURL getAuditUrl()
         return new ActionURL(AuditController.ShowAuditLogAction.class, ContainerManager.getRoot());
     }
 
-    public record TransactionRowIds(List<Long> rowIds, Map<Long, Long> dataTypeRowCounts) {}
+    public record TransactionRowIds(Set<Long> rowIds, Map<Long, Long> dataTypeRowCounts) {}
 
     public TransactionRowIds getTransactionSampleIds(long transactionAuditId, User user, Container container, @Nullable ContainerFilter containerFilter)
     {
@@ -267,8 +268,15 @@ public TransactionRowIds getTransactionSampleIds(long transactionAuditId, User u
                     .map(SampleTimelineAuditEvent.class::cast)
                     .toList();
         }
+        // Drop the secondary "added/removed sample to/from job" events; the same sample has a primary registration/update event in the transaction, so counting these would double-count it.
+        events = events.stream()
+                .filter(event -> SampleTimelineAuditEvent.SampleTimelineEventType.INSERT.getComment().equals(event.getComment()) || SampleTimelineAuditEvent.SampleTimelineEventType.MERGE.getComment().equals(event.getComment()))
+                .toList();
+
         Map<Long, Long> dataTypeRowCounts = new HashMap<>();
-        List<Long> sampleIds = new ArrayList<>();
+        // Return distinct set of sampleIds, since there might be multiple events in transaction for the same sample
+        // For example: job derive action creates one registration event, one add to job event.
+        Set<Long> sampleIds = new HashSet<>();
         events.forEach(event -> {
             dataTypeRowCounts.merge(event.getSampleTypeId(), 1L, Long::sum);
             sampleIds.add(event.getSampleId());
@@ -279,7 +287,7 @@ public TransactionRowIds getTransactionSampleIds(long transactionAuditId, User u
     public TransactionRowIds getTransactionSourceIds(long transactionAuditId, User user, Container container, @Nullable ContainerFilter containerFilter)
     {
         List<String> lsids = new ArrayList<>();
-        List<Long> sourceIds = new ArrayList<>();
+        Set<Long> sourceIds = new HashSet<>();
         Map<Long, Long> dataTypeRowCounts = new HashMap<>();
         List<AuditTypeEvent> transactionEvents = TRANSACTION_EVENT_CACHE.get(transactionAuditId).second;
         List<DetailedAuditTypeEvent> detailedEvents = transactionEvents.isEmpty()
diff --git a/query/src/org/labkey/query/controllers/QueryController.java b/query/src/org/labkey/query/controllers/QueryController.java
index 7bdffee8991..e1c9d69d2f5 100644
--- a/query/src/org/labkey/query/controllers/QueryController.java
+++ b/query/src/org/labkey/query/controllers/QueryController.java
@@ -4651,6 +4651,10 @@ protected JSONObject executeJson(JSONObject json, CommandType commandType, boole
             Map<String, Object> auditDetails = json.has("auditDetails") ? json.getJSONObject("auditDetails").toMap() : new CaseInsensitiveHashMap<>();
 
             Map<Enum, Object> configParameters = new HashMap<>();
+
+            if (extraContext.containsKey(AbstractQueryImportAction.Params.useTransactionAuditCache.name()))
+                configParameters.put(AbstractQueryImportAction.Params.useTransactionAuditCache, extraContext.get(AbstractQueryImportAction.Params.useTransactionAuditCache.name()));
+
             if (WorkflowService.get() != null)
                 WorkflowService.get().populateConfigParams(extraContext, configParameters);