I vary my play between 3 monitors (1x 2560x1440 (in the middle), 2x 1920x1080 (on the sides), sometimes full-screen and sometimes windowed (of various resolutions (, and sometime in VR). This seems to confuse where the pop-out windows (like ATC, navlog, VFR map, etc.) are displayed. Now, some of my mostly-used windows are not visible anywhere when I pop them out.
That happened to me, too. I think that they can be reset in the drop-down. I quit using pop-outs. Every one drain between 5 and 15 fps. External programs like LittleNavMap or vfrmap work better without performance hits.
I had the problem in September. I can’t remember exactly what I did to fix it. I couldn’t find anything in the forums, either. But it was a “forehead slapping moment” when I found the solution. It was obvious at the time and I thought that I’d should probably make a note of it. I decided that it was easier not to pop windows out. I really wish I could help. I remember being annoyed about it.