That is due to the swap I made in 3.6b3. In earlier versions, all the keyboard types were based on the original KCAP resources used in the classic Mac system, which worked with the origin in the top left of the screen. At some point (maybe around Mac OX X 10.4 Tiger) these disappeared from the system, and I created my own versions of them as binary files which essentially kept the resource format. In recent times, I converted these to an XML-based format, but didn’t convert the coordinate system, so that one step in creating the on-screen keyboard was to flip each key within the bounding rectangle. Since that was causing me trouble, and to make it easier to create your own keyboard types, I switched all of these XML files to have the coordinate system based on the lower left as part of the changes for 3.6b3.
So the point is that I should have made it clearer that these changes affected the way a user creates a keyboard type. The file within the Ukelele bundle has the files in the right format, so they can be used as the basis of a new keyboard type.
Anyway, I’m glad that you got it working!
John