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Windows 2008 R2 SP1. I stop the tomcat service and run the installer for 6.3.1. It runs and completes without error. Open the bamboo home/login page - it still shows version 5.7.2.
This article https://confluence.atlassian.com/display/BAMBOO0602/Bamboo+upgrade+guide says you can't upgrade directly using your existing install folder. Upgrading is really installing the new version to a new folder, and pointing it to your existing home directory. I recommend following the steps there, including the requirement/environment check , or perhaps Atlassian has a better procedure documented.
I think the best place to start will be the Bamboo logs. See if there was an issue with the upgrade and if it started but perhaps did not complete. If that is the case you should have a reason as to why.
When you find the relevant logs snippets if you need help figuring out what it means please post the snippet here and we'll go from there.
Thank you, Branden. I found an article suggesting I backup the machine, stop Bamboo, remove the service, rename the current install directory to OldBamboo, run the install as new but pointing it to the existing Bamboo home, copy the server config XML file from OldBamboo to the new install folder, install the service and start. This got me past this issue but I have other platform/environment issues to work out. I'll post this as an answer.