track ordering in IGV session file

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Daphne HSM

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Dec 8, 2025, 5:35:29 AM (5 days ago) Dec 8
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IGV version = 2.19.1

I can't seem to get the track ordering in my IGV session correct. My session contains several vcf tracks, a bed track, a bw track, a bam track, and a bedgraph track. The last one seems to give me problems. I want it at the top, and I ordered the tracks in my session xml file accordingly. However, when opening in IGV, the bedgraph track keeps getting placed at the bottom, while I want it at the top.
When I manually reorder the tracks in IGV, and put the bedgraph track as the second from the top (so it is different from my original session file and I can actually see if it changed), save as a new session, and open it again as a session in IGV, again it puts it at the bottom. Opening this newly saved session in a text editor, I do see that it is the second from the top in the newly saved session xml file. So my assumption is that there is some setting in my IGV desktop version that overrides the ordering in my session xml file. Does anyone know where to change this? Or have any idea what else might be the problem? I've tried many things, also putting it in a separate panel doesn't help. 

Thanks!
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