It is extremely common that one starts a feature or bug prior to actually starting the GitFlow process. This means there are often unstaged changes before starting a GitFlow bug/feature. When you do this, it will fail as there are uncommitted changes when it needs to change branch/make a branch/etc.
Unfortunately SmartGit isn't automatically stashing/unstashing in response to this. Which makes using GitFlwo very frustrating.
It should be no issue to stash all changes, perform the GitFlow process, then unstash.
Customer support service by UserEcho