WowAce

What steps will reproduce the problem?
1. Bring up map
2. Click C for config window

What is the expected output? What do you see instead?
  Config window should cover map. Instead, map covers config window.

What version of the product are you using?
  Cartographer 3 v0.9.1

I noticed this myself. As a short term fix, resize the top cartographer window so that you can see the configuration window. Change the map strata to medium. Then restore the map window's size.

Now the config window will be over the map, but your character window and such will also be over the map.

Arguably, this could be the default rather than the current default which (I have trouble remembering but I think it is fullscreen). In any case, it is also arguable that the dialog should be in a higher strata than the map,just as the placement of mapnotes has to be higher than the map.

Temporary solution: set the map strata to medium or lower.