I have had this issue a few times, especially after switching monitors and fiddling around with the display.
This solutions serves as my reference and also hopefully as a reference for anyone else struggling to find a solution online.
How to resolve the issue:
- Hold “Alt” + “Space”
- Choose move from the popup menu
- And then use your mouse cursor to move the window
- Close FileZilla and reopen it. It will now open in the last position it was saved.