While trying to upgrade from 3.11 to 3.13 an error was thrown while importing the XML backup and the system administration privilege would not be assigned to the jira-administrators group.

The problem seems to be specific to the customer data, and only when restoring on Windows when the index directory from the 3.11 backup cannot be created on the target machine. I can repeatedly reproduce the problem with the customer's backup. I've attempted to replicate myself by installing 3.11, creating issues, integrating fisheye, then exporting to JIRA 3.13 without success.

It looks like DataImport.java refreshes each of the plugins when the restore process is started. When the fisheye plugin would get reloaded, it would try to run a reindex on the old index directory, and throw an exception when the location of the old index directory cannot be created. This throws an exception and the import fails because its not caught (in the JIRA 3.13 branch). Looks like this is might be fixed in the trunk, by surrounding the code with try/catch/finally block around the refresh of the plugins and activating the new index directory in a finally block.