Hi @libby
Yes, the other sites are probably using a different release, possibly a patch release. Their release notes will likely list out the changes over time.
The default indexes in Galaxy are just one choice. If you would like to use a different genomic release version for follow up analysis in Galaxy, you could load up the genomic fasta file and use it as a custom genome. This method will work with most tools, and you could generate a custom database dbkey too, for cross-links with display applications like IGV.
If this interests you, please see → Custom genome + custom build: How to use a genome that is not natively indexed at the server you are working at - #2 by jennaj
Any questions with this, please ask! 