I found another slight error in the new default template.
According to this image, the two combos that I circled in red are set to "No Flying Enemies" by default, but those two combos happen to be a part of the Z1 Door Combo Sets. In other words, Link would step over them with the "Freeform Dungeons" rule turned on. They need to be reset to "Overhead" so that Link walks under them with the "Freeform Dungeons" rule turned on. They go to the Left and Right Doors. The Upper Combos of the Top Doors and Lower Combos of The Bottom Doors are set to "Overhead" by default, so all that needs to be fixed is the combos that I circled in red.
About a couple of combos in the default template
Whenever I find reported issues about something wrong in the Default Template, I act quickly to provide a blank.qst.
This fix will not only fix this issue but also will fix others in this thread: http://www.armageddongames.net/forums//thread/100796/
Here is the blank.qst, developers: Click
Fixed in the next build.