Why does my multiple alignment load as reference sequences?

Full question: 
When I have a multiple alignment in the multi-fasta format, it loads as independent references. How do I fix this?

This is most likely caused by an index file. If you want to have the multiple alignment visualization for a multi-fasta file, you should not have an index file.

Make sure that there is no file with the extension '.fai' with you fasta file.

If the problem persists, there may be an index file cached by GenomeView. You can remove cached index files by removing all files in the .genomeview/index folder in your home directory.