The branches drop down when switching branches in the repository view in Fisheye or selecting changesets in Crucible only shows the first fifty branches alphabetically.
Once you start typing, you can filter on any branch which is good, but it would be of more value if the branches listed were only the active ones. Right now we don't see most of our active branches in the drop down because there are lots of closed branches from a couple of years ago that start with the letter A or B, making the drop down pretty useless for us.
You may want to exclude all the other closed branches at Administration > Repository Settings > Repositories > reponame > Include/Exclude Paths
For more information, please refer to https://confluence.atlassian.com/display/FISHEYE/Include+Exclude+paths
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