To reproduce:
1.Create new project, import attached "repro" package.
2.Open and play "test" scene.
3.Notice in left-top corner - 3 GUI labels, click in the middle of pink sphere, ScreenToWorldPoint label will show 0,0,-10.
4.Build this scene for standalone, launch it in non-native resolution in fullscreen, try to repeat step 3.
5.Notice that ScreenToWorldPoint label will show wrong results.

Additional notes:
Going from fullscreen to windowed and back with alt+enter, causes strange behaviors to occur, like fullscreen clipping and selected resolution change.