Yeah I GODDAMMITSOMUCHed about the 1 hour wait between files a couple of days ago.
In the time since, I too have experienced the BS flooding of the servers error.
JD would go down the list, get the error for each file, and then stop at the end and not retry anything at all.
Happily, JD updated yesterday and it now recognizes the flooding error and waits to retry the same file instead of quickly trying all the files in the queue and then stopping at the end.
Basically, it now behaves the same way with the flooding message as it does with the "no more free slots available" message.