If you associate a build to an issue AFTER changing the project key you will not have permission to view it in JIRA.

Steps to repro:

• create on JIRA project
• link it to a Bamboo project
• create an issue from a build
• change the JIRA project key
• create another issue from a build

Expected results:
You should be able to view both as they have the same permissions

Actual results:
You get an error:
"You don't have access to view all related builds. Please contact your administrator."

I also noticed that looking at the build in Bamboo shows the old key and an error: "Could not obtain issue details from JIRA" and reindexing does not help.