I see what you guys are saying, but what I was thinking of really isn't that complex. (I hope...) I was just thinking of a little semi-independant app, like the scheduler. You could just add a bunch of sites, and if it gets in, it opens up a new copy of flashfxp with that connection. (Which I assume is the difficult part.)
And Shark, you're quite right about the ability to open up multiple copies of FlashFXP, I just find it kind of annoying when I'm trying to get into a lot of servers.
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