diff --git a/src/Ryujinx.Ava/Modules/Updater/Updater.cs b/src/Ryujinx.Ava/Modules/Updater/Updater.cs
index 77d77d794..839526c4e 100644
--- a/src/Ryujinx.Ava/Modules/Updater/Updater.cs
+++ b/src/Ryujinx.Ava/Modules/Updater/Updater.cs
@@ -740,6 +740,18 @@ namespace Ryujinx.Modules
         {
             var files = Directory.EnumerateFiles(HomeDir); // All files directly in base dir.
 
+            // Determine and exclude user files only when the updater is running, not when cleaning old files
+            if (_running)
+            {
+                // Compare the loose files in base directory against the loose files from the incoming update, and store foreign ones in a user list.
+                var oldFiles = Directory.EnumerateFiles(HomeDir, "*", SearchOption.TopDirectoryOnly).Select(Path.GetFileName);
+                var newFiles = Directory.EnumerateFiles(UpdatePublishDir, "*", SearchOption.TopDirectoryOnly).Select(Path.GetFileName);
+                var userFiles = oldFiles.Except(newFiles).Select(filename => Path.Combine(HomeDir, filename));
+
+                // Remove user files from the paths in files.
+                files = files.Except(userFiles);
+            }
+
             if (OperatingSystem.IsWindows())
             {
                 foreach (string dir in WindowsDependencyDirs)
diff --git a/src/Ryujinx.Ava/UI/Controls/ApplicationGridView.axaml b/src/Ryujinx.Ava/UI/Controls/ApplicationGridView.axaml
index f7a120b1a..3d55793f9 100644
--- a/src/Ryujinx.Ava/UI/Controls/ApplicationGridView.axaml
+++ b/src/Ryujinx.Ava/UI/Controls/ApplicationGridView.axaml
@@ -32,10 +32,10 @@
             <ListBox.ItemsPanel>
                 <ItemsPanelTemplate>
                     <flex:FlexPanel
-                        HorizontalAlignment="Stretch"
+                        HorizontalAlignment="Center"
                         VerticalAlignment="Stretch"
                         AlignContent="FlexStart"
-                        JustifyContent="Center" />
+                        JustifyContent="FlexStart" />
                 </ItemsPanelTemplate>
             </ListBox.ItemsPanel>
             <ListBox.Styles>
diff --git a/src/Ryujinx.Graphics.Gpu/Engine/Compute/ComputeClass.cs b/src/Ryujinx.Graphics.Gpu/Engine/Compute/ComputeClass.cs
index 8227a7ff1..d8103ac71 100644
--- a/src/Ryujinx.Graphics.Gpu/Engine/Compute/ComputeClass.cs
+++ b/src/Ryujinx.Graphics.Gpu/Engine/Compute/ComputeClass.cs
@@ -151,8 +151,6 @@ namespace Ryujinx.Graphics.Gpu.Engine.Compute
 
             ShaderProgramInfo info = cs.Shaders[0].Info;
 
-            bool hasUnaligned = _channel.BufferManager.HasUnalignedStorageBuffers;
-
             for (int index = 0; index < info.SBuffers.Count; index++)
             {
                 BufferDescriptor sb = info.SBuffers[index];
@@ -177,9 +175,17 @@ namespace Ryujinx.Graphics.Gpu.Engine.Compute
                 _channel.BufferManager.SetComputeStorageBuffer(sb.Slot, sbDescriptor.PackAddress(), size, sb.Flags);
             }
 
-            if ((_channel.BufferManager.HasUnalignedStorageBuffers) != hasUnaligned)
+            if (_channel.BufferManager.HasUnalignedStorageBuffers != computeState.HasUnalignedStorageBuffer)
             {
                 // Refetch the shader, as assumptions about storage buffer alignment have changed.
+                computeState = new GpuChannelComputeState(
+                    qmd.CtaThreadDimension0,
+                    qmd.CtaThreadDimension1,
+                    qmd.CtaThreadDimension2,
+                    localMemorySize,
+                    sharedMemorySize,
+                    _channel.BufferManager.HasUnalignedStorageBuffers);
+
                 cs = memoryManager.Physical.ShaderCache.GetComputeShader(_channel, poolState, computeState, shaderGpuVa);
 
                 _context.Renderer.Pipeline.SetProgram(cs.HostProgram);
diff --git a/src/Ryujinx.Graphics.Texture/SizeCalculator.cs b/src/Ryujinx.Graphics.Texture/SizeCalculator.cs
index 4ddd8d4df..0120bd7ac 100644
--- a/src/Ryujinx.Graphics.Texture/SizeCalculator.cs
+++ b/src/Ryujinx.Graphics.Texture/SizeCalculator.cs
@@ -90,6 +90,7 @@ namespace Ryujinx.Graphics.Texture
 
                 mipOffsets[level] = layerSize;
                 sliceSizes[level] = totalBlocksOfGobsInY * robSize;
+                levelSizes[level] = totalBlocksOfGobsInZ * sliceSizes[level];
 
                 if (is3D)
                 {
@@ -116,12 +117,15 @@ namespace Ryujinx.Graphics.Texture
                         // The slice only covers up to the end of this slice's depth, rather than the full aligned size.
                         // Avoids size being too large on partial views of 3d textures.
 
-                        sliceSizes[level] -= gobSize * (mipGobBlocksInZ - gobRemainderZ);
+                        levelSizes[level] -= gobSize * (mipGobBlocksInZ - gobRemainderZ);
+
+                        if (sliceSizes[level] > levelSizes[level])
+                        {
+                            sliceSizes[level] = levelSizes[level];
+                        }
                     }
                 }
 
-                levelSizes[level] = totalBlocksOfGobsInZ * sliceSizes[level];
-
                 layerSize += levelSizes[level];
 
                 depthLevelOffset += d;
diff --git a/src/Ryujinx/Modules/Updater/Updater.cs b/src/Ryujinx/Modules/Updater/Updater.cs
index 3e0dc99b4..344edf9e5 100644
--- a/src/Ryujinx/Modules/Updater/Updater.cs
+++ b/src/Ryujinx/Modules/Updater/Updater.cs
@@ -565,6 +565,18 @@ namespace Ryujinx.Modules
         {
             var files = Directory.EnumerateFiles(HomeDir); // All files directly in base dir.
 
+            // Determine and exclude user files only when the updater is running, not when cleaning old files
+            if (Running)
+            {
+                // Compare the loose files in base directory against the loose files from the incoming update, and store foreign ones in a user list.
+                var oldFiles = Directory.EnumerateFiles(HomeDir, "*", SearchOption.TopDirectoryOnly).Select(Path.GetFileName);
+                var newFiles = Directory.EnumerateFiles(UpdatePublishDir, "*", SearchOption.TopDirectoryOnly).Select(Path.GetFileName);
+                var userFiles = oldFiles.Except(newFiles).Select(filename => Path.Combine(HomeDir, filename));
+
+                // Remove user files from the paths in files.
+                files = files.Except(userFiles);
+            }
+
             if (OperatingSystem.IsWindows())
             {
                 foreach (string dir in WindowsDependencyDirs)