If you zoom in on the borders of the regions in the region editor you will notice that the borders do not completely enclose these cells. The cells are divided into quads (quarter of a cell), so if your border only passes through, say, the corner of the cell, only that quad will be painted with those textures. To paint the whole cell, the border has to completely enclose all four quads. This means that, since your regions butt up against each other, you will often have texture issues along the borders: either you won't include enough of the cell to paint all four quads or you will overlap into the next cell (with its own region data) and the generator will have to decide which textures to paint. Aside from very careful border placement, there is no way to avoid this issue (and if you use diagonal lines anywhere in your region--as most regions do--it is impossible to avoid). That's just one of the limitations of using the region generator.
At this point, there is probably no advantage in going back and re-generating your regions (glad it finally completed for you, btw
). Your best option is to tweak these problem cells by hand using the landscape editor. In any case, since they're transition areas, you'll probably want to control the transition by blending textures and object spawns. Everyone who uses region generation goes through this as part of the process. Have fun!
Object references (rocks, trees, etc.) don't suffer from this cell quad behavior, btw. The generator calculates objects based on the entire cell. Only landscape textures have this limitation.