According to https://confluence.atlassian.com/display/JIRA/Changing+the+Project+Key+Format it is possible to change the default project key format in jira.
Bamboo does not allow for a non-default Jira project key to be used. The parser will only filter the default format of [A-Z][A-Z]+ and ignore other patterns.
If JIRA has been modified to allow non default characters as part of the issue key:
and an issue key has been configured to contain non default char: TEST_TEST for example then the created JIRA link in Bamboo will be incomplete, seemingly truncated.
In this screenshot I happen to have an issue in JIRA with the key TEST-1 (in addition to TEST_TEST-1) and the bottom most link under JIRA issues links to the incorrect issue TEST-1 instead of the proper TEST_TEST-1. It seems somewhere in link creation/rendering that info is truncated and neither link points to the right place.
If this issue is fixed please update https://confluence.atlassian.com/display/AdminJIRAServer073/Changing+the+project+key+format and remove warning about Bamboo integration.