Sorry for the very late reply everyone, my participation here at the Guild has dwindled over the last couple of years due to increased responsibilities at home.
Hi Voolf, yes, you've correctly identified the issue. I was never really satisfied with this technique either due to the issues you raise. Waldronate once suggested a different method to me. In Wilbur you can use the River Flow filter (Texture > Other Maps > River Flow) to isolate just the rivers onto their own height map. On the pop-up menu that appears check the box for use solid background color (which should be black by default). The image should now be black except for your rivers. Now change the color of "River Mouth" to white and the color of the "River Source" to a mid grey tone (you can also play around with the sliders till you get the amount of river branching you desire); this will give you a nice gradient that can be used in the next step. Next go ahead and export this as a .png file and then open this as a new image in GIMP. Next, on your GIMP map file create a new "Rivers" layer (above your previous layers) and fill the entire layer with the color you wish your rivers to be. Following this, create a layer mask for this new layer. Now go ahead and copy the B&W river height map you just opened and paste it into the layer mask of your newly created Rivers layer. That's it; you should now have colored rivers.
Huh, that is very odd indeed. I'm trying to think of what might caused this, but I'm coming up empty here. So long as that layer was selected the curves should be operating on that layer. I'm sorry to not be of much help to you here but I just dunno what the trouble is.
Hey that's pretty good for a first effort! You've pointed out some areas that could be improved, but that all comes with practice. The more you play with the technique the more you'll develop a knack for this sort of stuff. Thanks for posting!
Cheers,
-Arsheesh