I have been encountering this issue for a while. I guess it came with the latest version of JCE.
Whenever I open the Link Manager, I find that the bottom edge of the window is outside the screen. To be more precise: the buttons [Cancel] and [Insert] are not directly accessible. I need to scroll down with the mouse in order to be able to click [Insert]. It seems as if the Link Manager enlarges the window beyond the bottom edge of the screen. See screenshot. Only the Link Manager is affected. The Image Manager working normally.
Thank you and kind regards
Chris