diff --git a/.github/workflows/scripts/compare_to_generic.sh b/.github/workflows/scripts/compare_to_generic.sh
index 59a1397ec5..8f046ec9d4 100755
--- a/.github/workflows/scripts/compare_to_generic.sh
+++ b/.github/workflows/scripts/compare_to_generic.sh
@@ -23,4 +23,32 @@ esac
 source_of_truth_modules="$base_dir/$source_of_truth/$modules_subdir"
 arch_modules="$base_dir/$target_arch/$modules_subdir"
 echo "Comparing $arch_modules to $source_of_truth_modules"
-python3 $script_dir/compare_stacks.py $source_of_truth_modules $arch_modules
+
+if ! python3 $script_dir/compare_stacks.py $source_of_truth_modules $arch_modules; then
+    echo "Warning: Comparison failed for CPU stacks" >&2
+    exit 1
+fi
+
+# Also compare NVIDIA GPU software stacks
+if [[ -n "$CUDA_COMPUTE_CAPABILITIES" ]]; then
+    read -ra compute_capabilities <<< "$CUDA_COMPUTE_CAPABILITIES"
+    echo "Also comparing CUDA-enabled software stacks (for compute capabilities: ${compute_capabilities[@]})"
+    # Initialize a variable to track failures
+    any_failure=0
+    # Loop over the array
+    for cc in "${compute_capabilities[@]}"; do
+        source_of_truth_modules="$base_dir/$source_of_truth/accel/nvidia/cc80/$modules_subdir"
+        arch_modules="$base_dir/$target_arch/accel/nvidia/$cc/$modules_subdir"
+        echo "Comparing $arch_modules to $source_of_truth_modules"
+        if ! python3 $script_dir/compare_stacks.py $source_of_truth_modules $arch_modules; then
+            echo "Warning: Comparison failed for compute capability $cc" >&2
+            any_failure=1
+        fi
+    done
+    if [[ $any_failure -ne 0 ]]; then
+        echo "One or more CUDA software stack comparisons failed." >&2
+        exit 1
+    fi
+else
+    echo "CUDA_COMPUTE_CAPABILITIES is not set or is empty, not checking NVIDIA software stacks"
+fi
diff --git a/.github/workflows/test_compare_stacks.yml b/.github/workflows/test_compare_stacks.yml
index 00c4af099a..f03929349b 100644
--- a/.github/workflows/test_compare_stacks.yml
+++ b/.github/workflows/test_compare_stacks.yml
@@ -8,11 +8,17 @@ on:
 permissions:
   contents: read # to fetch code (actions/checkout)
 env:
-  EESSI_ACCELERATOR_TARGETS: |
+  CUDA_COMPUTE_CAPABILITIES_YAML: |
+    # Provide a default set of compute capabilities
+    default:
+      - cc70
+      - cc80
+      - cc90
+    # and then allow for special cases for specific architectures
     x86_64/amd/zen2:
-      - nvidia/cc80
-    x86_64/amd/zen3:
-      - nvidia/cc80
+      - cc70
+      - cc80
+      - cc90
 jobs:
   compare_stacks:
     runs-on: ubuntu-24.04
@@ -53,4 +59,11 @@ jobs:
 
               # Compare the requested architecture to the generic stack
               # (assumes the general structure /cvmfs/software.eessi.io/versions/2023.06/software/linux/$COMPARISON_ARCH/modules/all)
+              # and include a check for CUDA-enabled software using the environment variable CUDA_COMPUTE_CAPABILITIES
+              # (which assumes the structure /cvmfs/software.eessi.io/versions/2023.06/software/linux/$COMPARISON_ARCH/accel/nvidia/$cc/modules/all)
+              
+              # Parse the yaml that makes the compute capabilities arch-dependent
+              CUDA_COMPUTE_CAPABILITIES=$(echo "${CUDA_COMPUTE_CAPABILITIES_YAML}" | yq ".\"${{matrix.COMPARISON_ARCH}}\" // .default | .[]" | tr '\n' ' ')
+              export CUDA_COMPUTE_CAPABILITIES=${CUDA_COMPUTE_CAPABILITIES%% }  # trim trailing space
+              
               .github/workflows/scripts/compare_to_generic.sh ${EESSI_PREFIX}/software/${EESSI_OS_TYPE} ${{matrix.COMPARISON_ARCH}}
diff --git a/easystacks/software.eessi.io/2023.06/accel/nvidia/rebuilds/20250926-eb-5.1.1-rebuild-lightGBM-for-cuda-sanity-check.yml b/easystacks/software.eessi.io/2023.06/accel/nvidia/rebuilds/20250926-eb-5.1.1-rebuild-lightGBM-for-cuda-sanity-check.yml
new file mode 100644
index 0000000000..8d75ed7190
--- /dev/null
+++ b/easystacks/software.eessi.io/2023.06/accel/nvidia/rebuilds/20250926-eb-5.1.1-rebuild-lightGBM-for-cuda-sanity-check.yml
@@ -0,0 +1,12 @@
+# We'll rebuild all CUDA software, for various reasons
+# 1. We now have a proper CUDA sanity check, and if anything was 'wrong' with our current CUDA installs, we'd like
+# to know about it
+# 2. The PR implementing a CI to check for differences between officially supported CUDA Compute Capabilities shows
+# that there are a lot of missing installations https://github.com/EESSI/software-layer/pull/1087 . A rebuild PR like
+# this will have the convenient side effect of filling all those holes
+easyconfigs:
+  - LightGBM-4.5.0-foss-2023a-CUDA-12.1.1.eb:
+      options:
+        # see https://github.com/easybuilders/easybuild-easyconfigs/pull/24023
+        from-commit: 853cdf7a8a3912aa0e55367b2b4451ebff00e13b
+        cuda-sanity-check-accept-missing-ptx: True