diff --git a/tests/functional_tests/python_test_utils/get_test_results_from_tensorboard_logs.py b/tests/functional_tests/python_test_utils/get_test_results_from_tensorboard_logs.py
index 7b74a6879ad..091623b9b84 100644
--- a/tests/functional_tests/python_test_utils/get_test_results_from_tensorboard_logs.py
+++ b/tests/functional_tests/python_test_utils/get_test_results_from_tensorboard_logs.py
@@ -1,3 +1,4 @@
+# Copyright (c) 2026 NVIDIA CORPORATION & AFFILIATES. All rights reserved.
 import os
 
 os.environ["OPENBLAS_NUM_THREADS"] = "1"
@@ -22,27 +23,13 @@
     help="Use first or all tensorboard logs",
     default=False,
 )
-@click.option(
-    "--is-second-run/--is-not-second-run",
-    type=bool,
-    help="Use second run of tensorboard logs",
-    default=False,
-)
 @click.option("--step-size", required=False, default=5, type=int, help="Step size of sampling")
 def collect_train_test_metrics(
-    logs_dir: str,
-    train_iters: str,
-    output_path: str,
-    is_convergence_test: bool,
-    is_second_run: bool,
-    step_size: int,
+    logs_dir: str, train_iters: str, output_path: str, is_convergence_test: bool, step_size: int
 ):
-    if is_convergence_test and is_second_run:
-        raise ValueError("Convergence test cannot be run on second run of tensorboard logs")
-
     summaries = common.read_tb_logs_as_list(
         logs_dir,
-        index=(-1 if is_convergence_test else (1 if is_second_run else 0)),
+        index=(-1 if is_convergence_test else 0),
         train_iters=train_iters,
         start_idx=1,
         step_size=step_size,
diff --git a/tests/functional_tests/shell_test_utils/run_ci_test.sh b/tests/functional_tests/shell_test_utils/run_ci_test.sh
index 0b360530b7d..efd4f08f2b3 100644
--- a/tests/functional_tests/shell_test_utils/run_ci_test.sh
+++ b/tests/functional_tests/shell_test_utils/run_ci_test.sh
@@ -226,6 +226,11 @@ for i in $(seq 1 $N_REPEAT); do
     FILE=$(basename "$_TENSORBOARD_PATH")
     export TENSORBOARD_PATH=$DIR/$i/$FILE
     mkdir -p $(dirname $TENSORBOARD_PATH)
+    # Per-repeat base; for ckpt-resume / frozen-resume tests each training
+    # phase writes to its own ${_REPEAT_TENSORBOARD_PATH}/run_N subdir so the
+    # analyzer can read by explicit path rather than guessing phase from
+    # mtime-sorted glob order.
+    _REPEAT_TENSORBOARD_PATH=$TENSORBOARD_PATH
     export REPEAT=$i
 
     wait_for_all_nodes "repeat_${REPEAT}_start"
@@ -294,6 +299,10 @@ for i in $(seq 1 $N_REPEAT); do
         done
     else
         # The standard single-run test that otherwise runs
+        if [[ "$TEST_TYPE" == "ckpt-resume" || "$TEST_TYPE" == "frozen-resume" ]]; then
+            export TENSORBOARD_PATH="$_REPEAT_TENSORBOARD_PATH/run_${RUN_NUMBER}"
+            mkdir -p "$TENSORBOARD_PATH"
+        fi
         run_training_phase "repeat_${REPEAT}_run_${RUN_NUMBER}"
     fi
 
@@ -316,6 +325,8 @@ for i in $(seq 1 $N_REPEAT); do
         echo $((TRAIN_ITERS / 2)) >$CHECKPOINT_LOAD_PATH/latest_checkpointed_iteration.txt
 
         export RUN_NUMBER=2
+        export TENSORBOARD_PATH="$_REPEAT_TENSORBOARD_PATH/run_${RUN_NUMBER}"
+        mkdir -p "$TENSORBOARD_PATH"
         run_training_phase "repeat_${REPEAT}_run_${RUN_NUMBER}"
     fi
 
@@ -326,6 +337,8 @@ for i in $(seq 1 $N_REPEAT); do
         export CHECKPOINT_SAVE_PATH=/tmp/checkpoints/
 
         export RUN_NUMBER=2
+        export TENSORBOARD_PATH="$_REPEAT_TENSORBOARD_PATH/run_${RUN_NUMBER}"
+        mkdir -p "$TENSORBOARD_PATH"
         run_training_phase "repeat_${REPEAT}_run_${RUN_NUMBER}"
 
         export CHECKPOINT_SAVE_PATH=$_CHECKPOINT_SAVE_PATH
@@ -371,8 +384,13 @@ for i in $(seq 1 $N_REPEAT); do
         # Read test values from Tensorboard for non-inference tests.
         # Inference tests will load from JSON instead.
         if [[ "$MODE" == "pretraining" ]]; then
+            if [[ "$TEST_TYPE" == "ckpt-resume" || "$TEST_TYPE" == "frozen-resume" ]]; then
+                FIRST_RUN_TENSORBOARD_PATH="$_REPEAT_TENSORBOARD_PATH/run_1"
+            else
+                FIRST_RUN_TENSORBOARD_PATH="$TENSORBOARD_PATH"
+            fi
             uv run --no-sync python $ROOT_DIR/tests/functional_tests/python_test_utils/get_test_results_from_tensorboard_logs.py \
-                --logs-dir $TENSORBOARD_PATH \
+                --logs-dir $FIRST_RUN_TENSORBOARD_PATH \
                 --train-iters $TRAIN_ITERS \
                 --output-path ${OUTPUT_PATH}/$(basename $GOLDEN_VALUES_PATH) \
                 "${EXTRACT_ARGS[@]}"
@@ -424,10 +442,9 @@ for i in $(seq 1 $N_REPEAT); do
 
                 if [[ "$TEST_TYPE" == "ckpt-resume" || "$TEST_TYPE" == "frozen-resume" ]]; then
                     uv run --no-sync python $ROOT_DIR/tests/functional_tests/python_test_utils/get_test_results_from_tensorboard_logs.py \
-                        --logs-dir $TENSORBOARD_PATH \
+                        --logs-dir "$_REPEAT_TENSORBOARD_PATH/run_2" \
                         --train-iters $TRAIN_ITERS \
                         --output-path "${OUTPUT_PATH}/$(basename $GOLDEN_VALUES_PATH .json)_2nd.json" \
-                        --is-second-run \
                         "${EXTRACT_ARGS[@]}"
                             
                     echo "Running pytest 1st vs 2nd run comparison"