Instead of using that program to merge the images, I've started using photoshops "Photo Merge" feature which isn't perfect but saves a lot of time since it can "snap" matching shapes into place when it doesnt get it right automatically
I record an AVI using raw video, then take that into VirutalDub, were I set it to only give me 2 frames a second (decimate by 30).. then I cherry pick frames which will allow me to build the room, import those into photoshop and use the merge tool. It's still slow but a lot faster than screen shotting every room and then stitching every image together manually
This game is a lot more fun once you start to understand the maps..