If you can detect the situation then this can be solved in very simple manner. The question is which point to choose as start point for floodfill. The simple answer is: try all of them. Of course it makes a sense to start only with points adjacent to the one where your cursor is located. In this case you will have at most 8 points to check. Even better - at least 2 of them are definitely painted already if current point forms a polygon.
So you have 8 points to check. Launch floodfill 8 times starting from each of those points.
Two things which you probably should keep in mind:
You should try filling the area in cloned version of your field in order to be able to get back if floodfill will not find a polygon.
Launching floodfill second time and later you should reuse this cloned version of your field to see whether it was filled there. This will allow you to check every point at most once and this will make your 8 floodfills almost as fast as 1 floodfill.