I did the following on a simple cube too, same problem.

The texture is a 1024x1024 tga file.
"flip texture horizontally" is selected.
Several faces to be textured are selected.
UV Map Selection
The preview window shows that the texture is not properly oriented.
Press OK : the applied texture is not properly oriented (the door handle should be towards the front).

The texture flip works with the paint tool.

The texture won't be shown flipped. I can't check right now, but doesn't the unwrap operation flip it when applied to the object?

Yes, you are right, the UVMap operation doesn't flip the UV coordinates. I've put this on my list.