1. Open default project.
2. Select file->save as....
3. Type file.01 in the file name textbox.
4. Deselect textbox or click save.
5. File name now appears as file.blend instead of the correct file.01.blend.
This seems to be consistent across all save dialogs, not just the blender project save. I often save files with numerical parameters in the file name, and this makes it inconvenient to do so.
Windows 7 SP1 64-bit
Blender 2.59.0 r39307 64-bit