When cloning from a page with a self signed certificate, fossil asks twice if an exception should be made. This is even with saying yes to remember the exception. The reason is the changed behavior in commit dc97155ec7 which calls autosync before opening a repository. What happens is that clone calls open but somehow the exception hasn't made it to the disk yet. An easy workaround is to simply pass --nosync to the open subprocess. But this is not ideal e.g. if the rebuild takes very long some commits made in that timeframe might be missed in the open clone.

Index: src/clone.c
==================================================================
--- src/clone.c
+++ src/clone.c
@@ -299,10 +299,11 @@
     blob_append_escaped_arg(&cmd, g.nameOfExe, 1);
     blob_append(&cmd, " open ", -1);
     blob_append_escaped_arg(&cmd, zRepo, 1);
     blob_append(&cmd, " --workdir ", -1);
     blob_append_escaped_arg(&cmd, zWorkDir, 1);
+    blob_append(&cmd, " --nosync ", -1);
     if( allowNested ){
       blob_append(&cmd, " --nested", -1);
     }
     fossil_system(blob_str(&cmd));
     blob_reset(&cmd);