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Hi Shawn,
Was it the new Oncorhynchus mykiss (assembly Omyk_1.0) ?
If you add a FASTA file from a new assembly to Genomebrowse, an assembly file gets created which specifies the order of the chromosomes listed. By default these chromosomes are sorted by size and not by number. If you want to edit the order in which these are displayed, you will have to edit the assembly file. This is typically found in your user data folder. To access this folder from GenomeBrowse, you can click tools > Open Folder > Annotations folder. Then back-up one directory to find the Assemblies folder. you can open the assemblies file in a text editor and change the order of the chromosomes.
