When I set up the combo yeast/mammalian mappings (e.g. mm10_sacCer3), I renamed the yeast chromosomes to "chrsc" instead of "chr" to ensure they would never conflict. So yeast-only mappings will display in the browser, but the yeast/mammalian ones are only visible in the mammalian genome. While there don't appear to be any current yeast/mammalian chromosome name conflicts, there might have been another issue with the browser.
When I set up the combo yeast/mammalian mappings (e.g. mm10_sacCer3), I renamed the yeast chromosomes to "chrsc" instead of "chr" to ensure they would never conflict. So yeast-only mappings will display in the browser, but the yeast/mammalian ones are only visible in the mammalian genome. While there don't appear to be any current yeast/mammalian chromosome name conflicts, there might have been another issue with the browser.