Had the same issue. When starting Keyboard Maestro the palettes that I have at the bottom move up by the height of the doc.
I just found a fix for this.
First install this plugin.
Then you can make a macro like this, that at engine start sets the position of your palette. (Palette name and position you will have to change of course and repeat the action for all your palettes) reposition macros.kmmacros (2.1 KB)