Yeah thats what happens with all 35mm adapters (without flip units anyway) its just an annoying side effect of adding another lens.
In final cut pro and other similar NLE systems you can flip it over pretty easily. In Final cut pro, you double click into the viewer, click the motion tab then dial the little clock icon round to 180 degrees....
Its under one of the effects, unless there is a quicker way, you have to apply the "effect" to each clip and tell it to rotate 180 degrees, or flip vertically. There are a number of ways to go about it