I don't understand what's the point of these annoying dialog boxes: it could be added an option at the preferences for the default behavior.
Avidemux < 2.6 is frame based editor, not really suited for HD video. Development on avidemux 2.5.6 was halted more then 3 years ago, last release was Version 2.5.6 (Dec 31, 2011)
Avidemux => 2.6 is a time based video editor, orientated towards HD video and the newer codecs.
SD video can be edited with avidemux 2.5.6, if the used codecs in the video are supported.
HD should be edited with avidemux 2.6