Ctrl-L will load the newest quicksave, but both should be displayed in the load screen. It shouldn't matter if you have other games on the go.
Check the number of files in the saved game folder that is not showing up (in '..\Divine Divinity\Run\savegames'). A new game should have 22 files, after going to either Verdistis or the Dark Forest it should have 27 and after going to both it should have 32...
Different file extensions are associated with different areas of the game;
.0 / .x0 = Aleroth, Ars Magicana, etc
.1 / .x1 = Verdistis, Council Hall
.2 / .x2 = Dark Forest