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I'm sure missing something. Can't really reproduce the extra beat in the MIDI metronome measure. Can you trace the MIDI events with aseqdump and verify you get something like this (Beats/Bar=4) :

Source  Event                  Ch  Data                                         
  0:1   Port subscribed            130:0 -> 129:0                               
130:0   Note on                 9, note 76, velocity 96                         
130:0   Note off                9, note 76, velocity 0                          
130:0   Note on                 9, note 77, velocity 64                         
130:0   Note off                9, note 77, velocity 0                          
130:0   Note on                 9, note 77, velocity 64                         
130:0   Note off                9, note 77, velocity 0                          
130:0   Note on                 9, note 77, velocity 64                         
130:0   Note off                9, note 77, velocity 0
130:0   Note on                 9, note 76, velocity 96
130:0   Note off                9, note 76, velocity 0
130:0   Note on                 9, note 77, velocity 64
130:0   Note off                9, note 77, velocity 0
130:0   Note on                 9, note 77, velocity 64
130:0   Note off                9, note 77, velocity 0
130:0   Note on                 9, note 77, velocity 64
130:0   Note off                9, note 77, velocity 0
130:0   Note on                 9, note 76, velocity 96
130:0   Note off                9, note 76, velocity 0

seeya

[EDIT: Whoa! Stop the press: I've noticed a glitch: sometimes, well, pretty repeatable, there's these duplicated MIDI metronome events being queued. This might be related to your problem, maybe not. Wonder why linuxsampler offsets duplicated note events (most MIDI sound modules I tested seem to ignore dupes, but I just might be lucky:). Check that out on qtractor 0.3.0.1193+ from CVS.]