If JIRA has been modified to allow underscores as part of the issue key:

and an issue key has been configured to contain an underscore: TEST_TEST for example then the created JIRA link in Bamboo will be incomplete, seemingly truncated.

JIRA Issue:

Bamboo link:

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.