Thank you for your bug report.
I have confirmed this bug, However this bug is caused by the treeview tool tip that appears when the site name is too long to display. When the tooltip is active and the site manager window closes the parent of the tooltip is invalid so the focus changed from FlashFXP to the next window.
To solve this problem I changed FlashFXP to turn off the tooltip before closing the site manager.
Yes, We are currently rewarding bug reporters with license keys. I will contact you via a private message.
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