I'm assuming this is a bug in igv.js, but here is a simple sequence of steps to reproduce it using the IGV-Web app
select a reference genome from the menu
select some other genome
select again the same genome as in step 1. (Note it has to be a genome you've selected before in the menu, not just the default genome the app started with)
I'm assuming this is a bug in igv.js, but here is a simple sequence of steps to reproduce it using the IGV-Web app
=> another sequence track is displayed.