When using an ExtensionFilter with FileChooser the default Windows behaviour is not observed. For example in notepad.exe if you choose to save a file and type "test" in the name box and a file by the name of "test.txt" already exists, then you get the overwrite warning. With JavaFX you don't. You must type the full name "text.txt" to get the warning. Also note that the File returned in JavaFX 2.2.7 does not include the extension of the selected filter, but in Lombard it does.

Combined with RT-28289 on JavaFX 2.2.7 it is not possible to determine the full filename that the user really wanted.
On Lombard and JavaFX 2.2.7 the overwrite warning must be hacked in after the dialog is dismissed.

See also RT-15422 and RT-28289