diff --git a/libs/storage/Tsavorite/cs/src/core/Index/Checkpointing/StateMachineDriver.cs b/libs/storage/Tsavorite/cs/src/core/Index/Checkpointing/StateMachineDriver.cs
index b6edc09960e..de614eca4fe 100644
--- a/libs/storage/Tsavorite/cs/src/core/Index/Checkpointing/StateMachineDriver.cs
+++ b/libs/storage/Tsavorite/cs/src/core/Index/Checkpointing/StateMachineDriver.cs
@@ -66,6 +66,12 @@ void DecrementActiveTransactions(long txnVersion)
 
         internal void TrackLastVersion(long version)
         {
+            // Only create and enqueue one semaphore per version, if we create a
+            // new one on each call, the earlier semaphore is orphaned in the waitingList
+            // and never released, and we permanently block ProcessWaitingListAsync.
+            if (lastVersion == version)
+                return;
+
             if (GetNumActiveTransactions(version) > 0)
             {
                 // Set version number first, then create semaphore
diff --git a/libs/storage/Tsavorite/cs/test/StateMachineDriverTests.cs b/libs/storage/Tsavorite/cs/test/StateMachineDriverTests.cs
index 51c205b76b2..396423c818b 100644
--- a/libs/storage/Tsavorite/cs/test/StateMachineDriverTests.cs
+++ b/libs/storage/Tsavorite/cs/test/StateMachineDriverTests.cs
@@ -401,4 +401,57 @@ public async ValueTask GrowIndexVersionSwitchTxnTest(
             [Values] bool useTimingFuzzing)
             => await DoGrowIndexVersionSwitchEquivalenceCheck(indexSize, useTimingFuzzing).ConfigureAwait(false);
     }
+
+    /// <summary>
+    /// Regression test for checkpoint deadlock with two-store checkpoints.
+    ///
+    /// TrackLastVersion is called once per store during the IN_PROGRESS phase.
+    /// Without the fix, the second call overwrites lastVersionTransactionsDone,
+    /// orphaning the first semaphore in the waitingList. ProcessWaitingListAsync
+    /// then waits on it forever.
+    /// </summary>
+    [AllureNUnit]
+    [TestFixture]
+    public class TrackLastVersionTwoStoreDeadlock : AllureTestBase
+    {
+        [Test]
+        public async Task TrackLastVersionCalledTwiceDoesNotDeadlock()
+        {
+            var epoch = new LightEpoch();
+            try
+            {
+                var driver = new StateMachineDriver(epoch);
+
+                // Simulate an active transaction (e.g. Lua script touching both stores)
+                var txnVersion = driver.AcquireTransactionVersion();
+
+                // GlobalAfterEnteringState calls TrackLastVersion once per store
+                driver.TrackLastVersion(txnVersion);  // MainStore
+                driver.TrackLastVersion(txnVersion);  // ObjectStore
+
+                // Transaction completes
+                driver.EndTransaction(txnVersion);
+
+                // Verify all waitingList semaphores are released (not orphaned)
+                var waitingList = (System.Collections.Generic.List<System.Threading.SemaphoreSlim>)
+                    typeof(StateMachineDriver)
+                        .GetField("waitingList", System.Reflection.BindingFlags.NonPublic | System.Reflection.BindingFlags.Instance)
+                        .GetValue(driver);
+
+                ClassicAssert.AreEqual(1, waitingList.Count,
+                    "Expected 1 semaphore in waitingList, not 2. " +
+                    "Two means the second TrackLastVersion call created a new semaphore " +
+                    "that overwrote the first, orphaning it.");
+
+                var acquired = await waitingList[0].WaitAsync(System.TimeSpan.FromSeconds(5));
+                ClassicAssert.IsTrue(acquired,
+                    "Semaphore was not released after EndTransaction. " +
+                    "This causes ProcessWaitingListAsync to deadlock permanently.");
+            }
+            finally
+            {
+                epoch.Dispose();
+            }
+        }
+    }
 }
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