I do not know what triggers this, but this has happened a few times where the custom window will move itself to the top left of runner screen and its size very small and overlapping the options there on the tool bar File/Edit/View is not visible, macro/window/help is.
Resetting tool bar doesn't change anything. Closing and restarting the game from Dev doesn't change anything either. This happened to me twice today (and in the past when using custom windows) and it came right for some reason, between testing my game in other areas.
This custom window usually sits on top of my other custom window to the right of screen and has been doing so for many test runs. So whether this is more prone to happen when there are two custom windows. I tried turning map on and off, graphics window on and off and the problem still persists.
This is a serious bug/problem if you need more than one custom window, it is an eye sore and the information within it is not readable.
The tiny custom window has a scroll bar, is heavily zoomed in and you cannot see the top of its window where there would be a pin or an x. The top of said window is slightly underneath the top of the toolbar.
The only way to manually fix this is to remove the custom window code and contents, save and then paste it back in. Still this problem could rare up post release of a game that uses custom windows.
Another update. I just tried to fix the issue again with this manual fix and it is not working. Where as it did before. Whether this fix is a hit and miss thing i don't know. I tried closing and restarting the Dev before pasting back in the probmatic custom window code no change.
Note: I should of said earlier the problem happens when there is a second custom window or more.
Doing some more testing, with these two custom windows. If i close the runner completely between running tests and running it again from Dev the custom windows display correctly with the odd time a third window (unintended window) appearing as a small window on top left of window as mentioned in this bug report earlier. If i 'restart' runner from within Runner this is when the bug i mention appears consistently.