JIRA v5.1.1
Confluence 4.3
MySQL 5.5
I set up a new server (test server) with the exact same version of JIRA and MySQL, as well as confluence. I then dumped the SQL databases from the old server and imported them on the new server. I also copied the following folders/files from the old server and overwrote the new servers files:
C: Program Files Atlassian Application Data JIRA data
C: Program Files Atlassian Application Data JIRA structure
C: Program Files Atlassian JIRA atlassian-jira images
C: Program Files Atlassian Application Data JIRA dbconfig.xml
C: Program Files Atlassian Application Data Confluence confluence.cfg.xml
C: Program Files Atlassian Application Data Confluence config
C: Program Files Atlassian Application Data Confluence index
Then, I started JIRA and Confluence and install plugins. Everything appears to be running properly except that I no longer have all my issues in JIRA. Oddly, 3 very old issues show up, but no other issues are present. The users, projects, greenhopper sprints, etc. are correctly pulled from the SQL database, but the issues are not.
I have investigated the contents of the SQL database and it does contain all the issues.