The duplicate logs tool doesn't update immediately. Project-GC doesn't receive notifications about log deletions or log edits, so it may take a while before we notice such things. For this particular case, you can speed up the process by clicking Support -> Self-support and then requesting a refresh of the GC codes where you have deleted logs.
As for the other issues you talk about, could you send a couple of examples (GC codes and usernames) where those type of problems appear?
