This does not appear to be a problem with the background color.

Fixed on trunk.

OK... using the bookmarks I gave you before (imported):

test1 - a scene containing .bam, .bed, .wig and ref sequence tracks in all default colors
color test - each track has a different FG color
bg color test - same fg colors as color test, but with a lilac background
devo test - the same as bg color test, but the name of every track was changed
test part 2 is a new scene using the same data in default colors/name.

If you load a bookmark from scratch (ie the first time the data gets loaded) it properly assigns color. the 'devo' bookmark will even cause the graph track to remember the user assigned name. This all works right.

BUT if you switch between bookmarks, it goes wrong... so,

1) open a fresh IGB, import the test bookmarks
2) open bookmark 'devo'
3) open bookmark 'test part 2'. Notice that the .wig and the .bed return to normal. .bam however has the bg and fg color from the last bookmark.
4) now open 'test1'. Notice that all track LABELS return to the proper starting color, but the .bam track fg remains red
5) Now open bookmark 'color test'. Notice that the track LABELS turn the proper color but the tracks themselves do not (although .bam remains red)
6) now open 'bg color test'. notice that the bg color change works right!
7) At this point if you reselect test 1, all BG reverts to black (properly) BUT if you select test part 2 the BG color of the bam track does NOT revert.

Is this still an issue for you? I imported your bookmarks, but it keeps freezing when I open the devo bookmark and the window pops up for username and password. It looks as if its loading but I cant click on anything.

I tested this with my own bookmarks though and it does not seem to be an issue now.

Windows 12043

FAILED V.13814, Mac, Java 1.7.0_10

Using Homo sapiens Feb, 2009, a bookmark was created with 3 tracks consisting of 2 VCF files and 1 RefGene track.

• Foreground and Background colors where changed for each track
• A bookmark was made with these colors saved
• Within the saved bookmark, the all track colors were changed again, then a new bookmark was made
• Selecting and opening the first bookmark produced expected results, with the proper colors appearing for track labels, the track, and the track background
• Selecting and opening the second bookmark produces UNEXPECTED results, with the colors of the track labels changing to the correct colors, but the colors of the tracks remaining as the colors of the first bookmark. The backgrounds do change according to the proper bookmark though.

Color out of sync is a known bug and cannot be fixed at present.