I'm using Eclipse with Egit/Github and Maven on Windows. Often but not always, when checking out a branch an error message is thrown indicating the pom.xml file could not be renamed which causes the checkout to fail. The file is locked by Windows, preventing the rename. Using Handle as suggested below shows Eclipse has the lock. Colleagues don't see this problem. I've installed an entirely different instance of Eclipse and cloned the repository to a different location and have the same results.
This all causes a great mess in my repository because Git does not have a rollback function on the checkout failure. All of the files from the go-to branch were copied in but git keeps the come-from branch as checked out. All of the files that differ between the branches are shown as modified. Cleanup takes a bit of work.