Erm, well let's see...
Apple changed approximately 219289798392 things in Lion

Even in Yummy FTP v1.8.4 (that pre-dates Lion) this problem occurs in Lion when there was never such a problem before in Snow Leopard, Leopard, Tiger, Panther, or Jaguar - yes, Yummy has been working correctly since Mac OS X 10.2
It's very clear that this problem is caused by a change in Lion, and I would call that a bug. Why on earth it only affects Yummy I'm not sure, but it's not my fault either - Yummy is doing nothing wrong!
That said, I obviously want to help resolve this issue, whether it's by creating some kind of work around in my code or by logging a bug with Apple. The problem I have is that I cannot repeat this issue despite having tried to on several different Macs.
So, until I have a repeatable case I cannot file a bug report with Apple nor can I try to find a work around. What can I do?? I guess I'll re-test this. Maybe I've missed some clue somewhere.
For what it's worth, in the v1.8.6 build that is coming soon, I've added a new preference option to disable the window auto-restore feature of Lion that forces the re-opening of FTP connection windows upon you. At least this eliminates some of the bizarre behavior caused by that feature that some people are seeing, although I have to say, I personally have not found any issues with it in my own usage.
I'll post back with my findings (if any) regarding the window activation problem.