In a glyph that has a component of another glyph in it, attempting to use the vertical mirror/flip in the Transformation palette panel, the transformation origin is ignored and seems to act as if the origin was set to half cap height. If “Disable Automatic Alignment” is set, then the transforms seem to work (at least testing the metrics origin setting).
This can also be seen going from a .glyphs file saved in 2.4.2 to 2.5b, the transform changes, e.g.,
-transform = "{1, 0, 0, -1, 0, 0}";
+transform = "{1, 0, 0, -1, 0, 750}";
Second line is the change after saving in 2.5b (1066).