An error crept into the interpretation of the MDR file format between Wilbur and FT3, resulting in the vertical flip that you see. Flip the map vertically in Wilbur using Surface>>Rotate>>Flip Vertically.

The height issues may be related to the world altitudes in FT, especially if you have an altitude sample or two that are extreme. If you know what the altitude range is supposed to be for the MDR file, use Wilbur's Filter>>Height Clip feature to force everything in the world to be between your desired low and high values (typically -10000 to +10000 for FT exports). You should be able to move your mouse over the land areas in Wilbur to get an idea of the heights. You can also use Window>>Histogram to get a direct count of the altitude values, which will give you an idea of you have extreme values and the approximate range of "normal" values.

Wilbur wants the file to have an MDR extension and you need to select the "MDR" file type in Wilbur's File Open dialog. If you didn't specify the extension in FT, then you'll need to rename the file in explorer for best results.