I am having no issues with the vertical track height changing.

Windows v12159

Creating a new bug report for issue Lance reported here on 6/18, because it is causing a separate issue. IGBC-382

Can you test all of these situations on windows? These are all cases where the vertical height is disturbed... just run through all of the tests listed in the main bug and through this list of comments. Primarily, this bug shows up if you cause 1) annotations to shift to graphs or the reverse and 2) when you change some aspect of a graph (primarily floating) that causes the annotations to be redrawn...

Fixed in r12138.

also, if you change attributes of a floating track, the height is thrown off.

another:

• pristine IGB
• A thaliana
• IGB Quickload > RNA-Seq > Loraine Lab > Mixed Cold > SM > Reads > Control, Alignments
  (new track at top)
• move hairline to area with data (e.g. chr1 : 16128522)
• move zoom scroller at top to right until it passes autoload marker (you may have to
  move the hairline to a green block)
• as soon as you pass over the autoload marker, and the track color changes to background
  color (before it finishes loading), move the zoom scroller back to the left, past the
  marker
  the track will stay the background color
• when the detail finishes loading, the track does not change.
• if you select the track by click on the label on the left, the track does change
  some times this works sometimes not, you may have to do it a couple of times.

Also:
from IGBC-315
Start from a completely clean IGB. Do NOT select a species. Simply drag in the IGIS file.

[The track is scrolled off so the bottom does not show,
but the zoom slider is at the top, and the scroll bar
is hidden, as if the track were completely in view.]

2) Set view to tbi (to be sure the 'misaligned' view mode is not playing havoc with the image). Pick a spot within the data area and zoom in - ALL the way in. Notice that all of a sudden, the track color snaps to the top of the main view window. Zoom out and see that the track now occupies a thing section at the top of main view.

3). click the track label, and the main view snaps the track label to now match the heifht of the data, the coordinate axis moves up, and there is a large black area underneath. Using the vertical zoom at this point to try to readjust the image causes really weird behavior - zoom all the way out and then back in vertically and watch the image change. Hiral said this might be a repacking issue.

see also attachment gsnap4_index.png
the top track is only filled in the top 60%.
the bottom is black

many, many cases of the track heights being off
also see
https://igbjira.uncc.edu/jira/browse/IGBC-315
2) and 3)