This error comes from within the JIRA Mail Threading handler, it is apparent a bug (https://jira.atlassian.com/browse/JRA-43397) occurring in JIRA doesn't specifically cause problems and is not something JEMH can influence.
JEMH-1985 - Getting issue details... STATUS
2013-04-10 12:18:45,939 http-bio-8080-exec-3 ERROR admin 738x2904x1 846ipk 192.168.0.57 /secure/admin/jemh/JEMHTestCases!update.jspa [atlassian.jira.mail.MailThreadManagerImpl] Unable to parse incoming In-Reply-To header <JIRA.39172.1363848677055@jira0>