What exactly are you doing? No more than 4 or 5 clicks are required to add corrections. You simply add single black pixels or lines of pixels to the outer frame.
Personally, I use Photoshop to work, but if you don’t have one yet, this is an expensive investment. GIMP or Paint.NET can easily do the same (technically, even MS Paint, but I would not want this program to be at all), and they are free.
EDIT: Somehow they didn’t notice that you have already tried GIMP. Any new software will have some learning curve, especially if it contains more functionality. draw9patch is pretty much a minimal feature set, so it’s easy to use, but trust me when I say that it would be worthwhile just to improve your skills in GIMP or Paint.NET.
EDIT: Well, just wanted to say that I'm judging too fast here. I really used the draw9patch tool for minor modifications and testing of my NinePatches, which I did in Photoshop. The process of drawing a line in d9p is an absolute pain in the ass. I see that in your comment you said you tried Photoshop. What you can actually do to simplify this is to add guides (View> New Guide) to the desired pixels, and then just use a pencil tool with a brush size of 1px, click and hold at the beginning of the line, hold shift and then drag at the end of the line. However, Photoshop has an annoying error (at least when installing CS2) when choosing the wrong pixel at a very close approximation, so you may need to erase a few wandering pixels that end through the guides. I would make your black border as a separate layer to make the task easier.
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