I was at the Black Magga questline, first it said I had won the scenario, but in the end, I couldn't progress farther into the game. However, I'm on my fourth try at it, and I'm currently stuck at "roll to gain items" at the general store. I closed it and now I'm rolling for items. After rolling for items, It shows how many I got, however the issue comes after. It picks the one card that I get to draw and then the entire map area (background) becomes black, and all my cards are acting weird. I think I'm probably going to have to go through it again, but does anyone know a current fix?

Both are known bugs.  First, closing locations in the scenario Here Comes The Flood is unnecessary, so I recommend you don't close anywhere.  This is how you get around the General Store Close bug.  Second, the scenario ends when there are no more cards left in any location deck.  However, there's a bug where if you don't encounter the last card in the last location (i.e. it's eaten by Black Magga), you can't advance on to the next scenario, even if you achieved the scenario goal.

 

Both of these bugs are listed as Fixed in the notes for the next patch (1.0.3.5).