I think our problems maya be a bit different. I understand that for you, if you don't act right away at a table then FTP will stop reminding you about it. For me, the table needing my attention doesn't pop up and the window doesn't take focus. Whatever table I last clicked still retains focus.
Another way of illustrating it - Say I have 2 tables up. I click on table 1, then I pull up Safari, covering both tables. Then table 2 needs my attention, but since table 1 still has focus, table 1 pops up instead, with table 2 still behind safari.
I'm starting to think this is a glitch with ftp on macs or something.