Almost always, the first, lowest note in the bass line of each measure is supposed to be held for the entire measure, i.e. 4 beats/whole note.  
This arrangement has more or less three voices.  One for the melody, one for the baritone fluff to make the music more interesting, and one for the sustained bass.  
TuxGuitar doesn't allow 3 voices; it only supports 2 voices.

Track1 is in capo 4
Track2 is in capo 5
As for the .gp5 file, the rhythems and tablature are correct.  However, the written pitch of the notes in the score section does not accurately reflect the tablature, because TuxGuitar only allows for audio pitch, not comprehensive, transpositions for capo effects.

ctrl-shift-down and ctrl-shift-up are hotkeys for switching between track 1 and track 2 on the .gp5 for a near seemless reading experience while playing a guitar, at least on TuxGuitar.