When the size of the window 'Set Coordinate System' (CTS plugin) exceeds the screen size, there doesn't show up a scrollbar, to get access to the hidden part of the window.
this seems to be a problem with newer java versions and dependent on the OS.
Hence, I can't say if we gonna fix that as it is a Java bug.
however, gonna forward it to the devel list,
could you please attach a screenshot of such an occasion?