I setup a Crucible review(i.e. APcr-234) and linked it to JIRA issue: BN-12345. In JIRA, I opened BN-12345, selected the Review tab and it shows the APcr-234 review so the linkages are properly setup. I now "Edit Details" for APcr-234, delete the current BN-12345 link and relink with bn-12345 (i.e. lower case). The linkage to JIRA is setup and it shows up as BN-12345 (i.e. upper not lower case). When I refresh the JIRA Review tab, the APcr-234 review info disappears. When I repeat the "Edit Details" for APcr-234 and relink the review back to BN-12345 (i.e. back to upper case). Then refresh the JIRA Review tab and the APcr-234 review info reappears. Am I missing some sort of configuration (regex?) or is this a known or new problem?
Using JIRA 5.2.11 and Crucible 3.0.3
I think it is possible you are facing the bug described by https://jira.atlassian.com/browse/CRUC-6924, though in this bug the link is not actually created, but it fails during its creation.
I noticed the bug does not exist in a most recent version (3.5.3), but if your linking is not actually failing, without checking the logs I couldn't say for sure if this could be solved by an upgrade.
Either way please notice the Smart Commits document mentions that "Smart commits only support the default JIRA issue key format (that is, two or more uppercase letters, followed by a hyphen and the issue number, for example BAM-123)", so besides you are not using a Smart Commit to create the link, I'd still recommend to keep using it in uppercase.
I'm going to check this further to see if this is a different bug.