There are many many bugs being brought up by wandering around in the gff3, tabix indexed IGIS models. I will give you several of the first few - feel free to split them into sub tasks as needed.

Start from a completely clean IGB. Do NOT select a species. Simply drag in the IGIS file.

1). The screen shows a tbi indexed view, but 'view mode' is set to 'annotations'.

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. Console shows many many repetitions of:

Jun 14, 2012 2:36:49 PM com.affymetrix.genometryImpl.thread.CThreadHolder notifyStartThread
WARNING: Thread Thread[pool-9-thread-1,5,main] already has com.affymetrix.igb.shared.IndexedSemanticZoomGlyphFactory$IndexedSemanticZoomGlyph$1@131b4c5d, and is starting com.affymetrix.igb.shared.IndexedSemanticZoomGlyphFactory$IndexedSemanticZoomGlyph$1@65327777
Jun 14, 2012 2:36:49 PM com.affymetrix.genometryImpl.thread.CThreadHolder notifyEndThread
SEVERE: could not find thread for Loading details for IGIS Gene Models.gff region chr20:18156403-18157507
Jun 14, 2012 2:36:49 PM com.affymetrix.genometryImpl.thread.CThreadHolder notifyStartThread

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.