diff --git a/image_analysis/IndexAndRefine.cpp b/image_analysis/IndexAndRefine.cpp
index 7b9563f8..61b30861 100644
--- a/image_analysis/IndexAndRefine.cpp
+++ b/image_analysis/IndexAndRefine.cpp
@@ -108,20 +108,31 @@ IndexAndRefine::IndexingOutcome IndexAndRefine::DetermineLatticeAndSymmetry(Data
             // If space group and cell provided => enforce that symmetry in refinement.
             // If not => detect the symmetry from the lattice.
             if (sg && experiment.GetUnitCell()) {
-                // FFBIDX returns the lattice already in the reference setting, so use it
-                // as-is. De-novo indexers (FFT/FFTW) return an arbitrarily-oriented primitive
-                // cell that must first be reduced to the conventional setting, else enforcing
-                // the crystal system on mis-assigned axes rejects every frame. Centering is
-                // taken from the user's space group; niggli_class is left unassigned (0) - it
-                // is a property of the primitive cell incl. centering, which LatticeSearch
-                // cannot recover from a cell the user may have given centered (e.g. C2). A
-                // proper primitive-cell indexing path (CrystFEL-style) is deferred.
                 outcome.symmetry = LatticeMessage{
                     .centering = sg->centring_type(),
                     .niggli_class = 0,
                     .crystal_system = sg->crystal_system()
                 };
-                outcome.lattice_candidate = de_novo ? LatticeSearch(latt).conventional : latt;
+                // Place every frame's cell in ONE consistent setting for the whole dataset:
+                // mixed axis orders (e.g. [78,78,38] vs [38,78,78]) index the same reflection
+                // as different HKLs and cannot be merged. LatticeSearch gives the conventional
+                // setting when its detected symmetry agrees with the user's space group. On
+                // noisy frames it can instead pick an alternative Bravais setting (e.g. the
+                // sqrt2 C-centred description of a primitive tetragonal cell,
+                // [78,78,38]->[110,111,38]); there:
+                //   - FFBIDX already returns the reference setting (c-last), consistent with the
+                //     conventional frames, so its raw lattice is safe -> use it (FFBIDX neutral);
+                //   - de-novo indexers (FFT/FFTW) return a Niggli-primitive cell with a DIFFERENT
+                //     axis order (c-first) that would corrupt the merge -> reject the frame.
+                // niggli_class is left unassigned (0): it needs the primitive cell incl.
+                // centering, which LatticeSearch cannot recover from a (possibly centred, e.g.
+                // C2) user cell. A proper primitive-cell indexing path (CrystFEL-style) is deferred.
+                auto sym_result = LatticeSearch(latt);
+                if (sym_result.system == sg->crystal_system())
+                    outcome.lattice_candidate = sym_result.conventional;
+                else if (!de_novo)
+                    outcome.lattice_candidate = latt;
+                // else: de-novo + symmetry mismatch -> leave unset, frame is not indexed
             } else {
                 auto sym_result = LatticeSearch(latt);
                 outcome.symmetry = LatticeMessage{
@@ -136,7 +147,7 @@ IndexAndRefine::IndexingOutcome IndexAndRefine::DetermineLatticeAndSymmetry(Data
             // lattice to each accepted extra lattice. Candidates are materialized later
             // in RefineGeometryIfNeeded so they're rooted in the refined (and, for
             // monoclinic, reordered) main lattice.
-            if (indexer_result.lattice.size() > 1) {
+            if (outcome.lattice_candidate && indexer_result.lattice.size() > 1) {
                 auto ml_latt = MultiLatticeSearch(indexer_result.lattice);
                 for (auto &ml : ml_latt) {
                     if (outcome.extra_lattice_rotations.size() >= experiment.GetIndexingSettings().GetMaxExtraLattices())