diff --git a/client/src/components/Upload/DefaultBox.vue b/client/src/components/Upload/DefaultBox.vue
index 31722c9184a0..cba474744251 100644
--- a/client/src/components/Upload/DefaultBox.vue
+++ b/client/src/components/Upload/DefaultBox.vue
@@ -113,15 +113,15 @@ const queue = new UploadQueue({
 });
 
 /** Add files to queue */
-function addFiles(files) {
+function addFiles(files, immediate = false) {
     if (!isRunning.value) {
+        if (immediate || !props.multiple) {
+            eventReset();
+        }
         if (props.multiple) {
             queue.add(files);
-        } else {
-            eventReset();
-            if (files.length > 0) {
-                queue.add([files[0]]);
-            }
+        } else if (files.length > 0) {
+            queue.add([files[0]]);
         }
     }
 }
diff --git a/client/src/components/Upload/UploadContainer.vue b/client/src/components/Upload/UploadContainer.vue
index ba4fa08dbcc6..9c7fe5a742dc 100644
--- a/client/src/components/Upload/UploadContainer.vue
+++ b/client/src/components/Upload/UploadContainer.vue
@@ -112,7 +112,7 @@ const showRegular = computed(() => !props.formats || hasRegularExtension);
 const showRules = computed(() => !props.formats || props.multiple);
 
 function immediateUpload(files) {
-    regular.value?.addFiles(files);
+    regular.value?.addFiles(files, true);
 }
 
 function toData(items, history_id, composite = false) {
diff --git a/client/src/components/Upload/UploadModal.vue b/client/src/components/Upload/UploadModal.vue
index 8aca0acde0dc..762abcc9afc0 100644
--- a/client/src/components/Upload/UploadModal.vue
+++ b/client/src/components/Upload/UploadModal.vue
@@ -86,7 +86,6 @@ defineExpose({
         <UploadContainer
             v-if="currentHistoryId"
             ref="content"
-            :key="showModal"
             :current-user-id="currentUser?.id"
             :current-history-id="currentHistoryId"
             v-bind="options"
diff --git a/client/src/stores/notificationsStore.ts b/client/src/stores/notificationsStore.ts
index 49a58eac7efc..6a7837e67928 100644
--- a/client/src/stores/notificationsStore.ts
+++ b/client/src/stores/notificationsStore.ts
@@ -41,6 +41,7 @@ export const useNotificationsStore = defineStore("notificationsStore", () => {
                 loadingNotifications.value = true;
                 await broadcastsStore.loadBroadcasts();
                 await loadNotifications();
+                updateUnreadCount();
             } else {
                 const data = await loadNotificationsStatus(lastNotificationUpdate.value);
                 totalUnreadCount.value = data.total_unread_count;
@@ -72,6 +73,10 @@ export const useNotificationsStore = defineStore("notificationsStore", () => {
         return updateBatchNotification({ notification_ids: [notification.id], changes });
     }
 
+    function updateUnreadCount() {
+        totalUnreadCount.value = notifications.value.filter((n) => !n.seen_time).length;
+    }
+
     return {
         notifications,
         totalUnreadCount,
diff --git a/lib/galaxy/webapps/galaxy/services/history_contents.py b/lib/galaxy/webapps/galaxy/services/history_contents.py
index c0d99167baa8..985dc06387b6 100644
--- a/lib/galaxy/webapps/galaxy/services/history_contents.py
+++ b/lib/galaxy/webapps/galaxy/services/history_contents.py
@@ -496,7 +496,9 @@ def prepare_collection_download(self, trans, id: DecodedDatabaseIdField) -> Asyn
 
     def __stream_dataset_collection(self, trans, dataset_collection_instance):
         archive = hdcas.stream_dataset_collection(
-            dataset_collection_instance=dataset_collection_instance, upstream_mod_zip=trans.app.config.upstream_mod_zip
+            dataset_collection_instance=dataset_collection_instance,
+            upstream_mod_zip=trans.app.config.upstream_mod_zip,
+            upstream_gzip=trans.app.config.upstream_gzip,
         )
         return archive
 
diff --git a/lib/galaxy_test/selenium/test_uploads.py b/lib/galaxy_test/selenium/test_uploads.py
index cad193f97f6e..6ce9607ea02e 100644
--- a/lib/galaxy_test/selenium/test_uploads.py
+++ b/lib/galaxy_test/selenium/test_uploads.py
@@ -174,6 +174,36 @@ def test_upload_paired_list(self):
         self.history_panel_wait_for_hid_hidden(3)
         self.history_panel_wait_for_hid_hidden(4)
 
+    @selenium_test
+    def test_upload_modal_retains_content(self):
+        self.home()
+
+        # initialize 2 uploads and close modal
+        self.upload_start_click()
+        self.upload_queue_local_file(self.get_filename("1.sam"))
+        self.upload_paste_data("some pasted data")
+        self.wait_for_and_click_selector("button#btn-close")
+
+        # reopen modal and check that the files are still there
+        self.upload_start_click()
+        self.wait_for_selector_visible("#upload-row-0.upload-init")
+        self.wait_for_selector_visible("#upload-row-1.upload-init")
+
+        # perform upload and close modal
+        self.upload_start()
+        self.wait_for_and_click_selector("button#btn-close")
+
+        # add another pasted file, but don't upload it
+        self.upload_start_click()
+        self.upload_paste_data("some more pasted data")
+        self.wait_for_and_click_selector("button#btn-close")
+
+        # reopen modal and see 2 uploaded, 1 yet to upload
+        self.upload_start_click()
+        self.wait_for_selector_visible("#upload-row-0.upload-success")
+        self.wait_for_selector_visible("#upload-row-1.upload-success")
+        self.wait_for_selector_visible("#upload-row-2.upload-init")
+
     @selenium_test
     @pytest.mark.gtn_screenshot
     @pytest.mark.local
diff --git a/packages/build_packages.sh b/packages/build_packages.sh
index 249b9143df5c..dde18ce11324 100755
--- a/packages/build_packages.sh
+++ b/packages/build_packages.sh
@@ -10,14 +10,18 @@ cd "$(dirname "$0")"
 
 # ensure ordered by dependency dag
 while read -r package_dir; do
-    printf "\n========= RELEASING PACKAGE ${package_dir} =========\n\n"
-
+    if [ -z "$package_dir" ]; then
+        # Skip empty lines
+        continue
+    fi
+    printf "\n========= RELEASING PACKAGE %s =========\n\n" "$package_dir"
+    
     cd "$package_dir"
-
+    
     make clean
     make commit-version
     make dist
     make new-version
-
+    
     cd ..
 done < packages_by_dep_dag.txt