If the set of skipped packages (probably same for files) defined by the configuration exception panel is "too large" up2date will generate a warning message window (... packages are available but were not selected ...) that exceeds the height of the screen. The "OK" button (to continue) is at the bottom of the warning message window. Depending on the user's choice of window manager, it may not be possible to move the warning message window to expose the "OK" button so that the user can continue with the up2date process. It would be better if either (simple fix) the "OK" button were at the top of the warning message window rather than at the bottom, or else (fancier fix) if the list of available but not selected packages was an embedded scrolling list with the warning message window sized to fit the available screen real estate (or something similar).
we have made this area a scrollable listbox instead of a textbox for 6.2.