Quick Answer: This may be related to settings in Liquid Notes for the zoom level, using no clean arrangement that may lead to wrong detection of chords or simply represent the progression of chords in your arrangement.
Varying length of chords along the timelineWhen opening a project Liquid Notes performs a harmonic analysis of your arrangement which detects correlations between notes, chord boundaries, etc. The result of this analysis is presented in the user interface of Liquid Notes by vertical strips that represents chords.
It may happen that these chords have varying length along the timeline, which may be caused by different reasons. See below for more information on possible causes.
Progression of chords in your arrangementLiquid Notes' harmonic analysis merely identifies the chords in your arrangement, and displays them accordingly in the user interface. Assuming that you arrangement is 'clean' and the harmonic analysis performs without error, the varying length of chords can be related to the actual progression of chords in your arrangement.
Limit zoom level in Liquid NotesThere is a setting Limit zoom level in Liquid Notes that prevents chords from fading out if activated. This may cause the display of chords to look rather abnormal in the user interface. Read more about this setting here.
No clean arrangement providedLiquid Notes' harmonic analysis expects your arrangement to be 'clean' for it to be able to identify chords over your entire song correctly. A 'clean' arrangement is given when, for example, the different tracks in your arrangement are clearly separated, a chord track can be clearly identified, or a chord is distributed over several instruments, to name a few.
When opening a project Liquid Notes's track type analysis will warn you if it detected any 'errors' deemed as 'not clean' in your arrangement (Note: Not all 'errors' can be detected by the software.). In this case it will ask you to correct the 'errors' detected in your arrangement - if this is ignored, or if the software can't detect those errors when opening the project, this may lead to a wrong detection of chords and also varying length of chords along the timeline.
Merge identical chordsLiquid Notes also provides an option to merge identical chords when opening a project. This allows for faster editing of chords by merging them into one should your arrangement contain a progression of same chords. Not having opted to activate this setting may display a succession of chords in varying length, mixed with other chords in your arrangement that have same or similar length.
Read more about this setting in this article - http://re-compose.desk.com/customer/portal/articles/562250.