diff --git a/rhodecode/lib/utils.py b/rhodecode/lib/utils.py
--- a/rhodecode/lib/utils.py
+++ b/rhodecode/lib/utils.py
@@ -206,7 +206,7 @@ def get_repos(path, recursive=False):
 def is_valid_repo(repo_name, base_path, scm=None):
     """
     Returns True if given path is a valid repository False otherwise.
-    If scm param is given also compare if given scm is the same as expected 
+    If scm param is given also compare if given scm is the same as expected
     from scm parameter
 
     :param repo_name:
@@ -413,6 +413,11 @@ def repo2db_mapper(initial_repo_list, re
         raise Exception('Missing administrative account !')
     added = []
 
+#    # clear cache keys
+#    log.debug("Clearing cache keys now...")
+#    CacheInvalidation.clear_cache()
+#    sa.commit()
+
     for name, repo in initial_repo_list.items():
         group = map_groups(name)
         db_repo = rm.get_by_repo_name(name)
@@ -438,6 +443,11 @@ def repo2db_mapper(initial_repo_list, re
         elif install_git_hook:
             if db_repo.repo_type == 'git':
                 ScmModel().install_git_hook(db_repo.scm_instance)
+        # during starting install all cache keys for all repositories in the
+        # system, this will register all repos and multiple instances
+        key, _prefix, _org_key = CacheInvalidation._get_key(name)
+        log.debug("Creating cache key for %s instance_id:`%s`" % (name, _prefix))
+        CacheInvalidation._get_or_create_key(key, _prefix, _org_key, commit=False)
     sa.commit()
     removed = []
     if remove_obsolete:
@@ -455,10 +465,6 @@ def repo2db_mapper(initial_repo_list, re
                     log.error(traceback.format_exc())
                     sa.rollback()
 
-    # clear cache keys
-    log.debug("Clearing cache keys now...")
-    CacheInvalidation.clear_cache()
-    sa.commit()
     return added, removed