I'm in the process of migrating our production Confluence 4.3.0 to a new windows server:
I've got the new system up and running, but not all of the user installed plugins have migrated.
* System Info:
** Server live:
*** Ubuntu Linux 2.6.31-14-server; MySQL 5.1.37-1ubuntu5.
** Server test:
*** Windows Server 2008 R2 64 bit; MySQL 5.5.28.
* The version of Confluence is the same in both instances.
* I've used an XML backup performed when no other users are online.
* I've synced the home directories, excluding some variations in the {{confluence.cfg.xml}} (license, connection URL to isolate from live system)
Interestingly, many of the User-installed Plugins appear in the test server under System Plugins, and the Configuration sidebar has different options for plugins.