Well, a couple ideas: First, go back to an image where the brush behaves as expected. Examine both the image characteristics and the specific brush settings and see if you can note differences.
Second, you could post a screenshot of the brush settings and a 100% crop of the area you are working on -- maybe we can spot something.
Are you using a color-selective saturation? From your description it sounds like it. The only other thought I have is that saturation brush can only bring out color that is actually there -- it doesn't realy "brush in" color. If your color pick is in the right range, it should do the job of saturating that particular color, but if you are off you get uncertain results.
Another consideration: is this an image that you desaturated prior than trying to brush in restored saturation, like selective coloring? If so, be aware that there are different types of desaturation that can have different effects. If you slide the Saturation slider all the way back, then applying a saturation brush will have a muted effect. However, if you desaturate by pulling back all the Saturation sliders in the HSL panel then brush in saturation, the effect will be much stronger.
Finally, although you said you checked all the settings, I do occasionally miss something. I can have saturation set to 100, the flow all the way up, brush away just to find my density is way low. It doesn't hurt to double-check. And, do you check your mask overlay (press "o")? It can give a clue of brush behavior.
Let us know!