Not exactly a troubleshoot, but like to share how I solved the buzz.
I bought my Rogue second hand and have been using it for more than 10 years now. I also use string action fairly low and neck bow almost straight, so I live normally with light fretting noise. In fact, I use that clicking - almost slapped sound - as a different color for when I hit strings harder. But sometime ago the D started to buzz almost in a fretless like tone.
I tried raise strings height and increase neck bow, but the string should be set really high and this messed with other strings seting. I don't feel confortable playing strings that high, so it was not a proper solution. I've also checked fret levels, but it clearly wasn't the cause, too. Than I realised it was the saddle.
My Rogue's D string didn't sound exactly like a fretless but more like the kind of a sitar do, and the sitar's tone comes from the way its strings ratle over the saddle. Sitar bridges are large and slightly curved in a way the string buzzes when plucked harder and that was the tone I was getting. Don't know when, why or how saddle's groove was deformed (I can bet it was from bending strings at the saddle to improve intonation, but not sure). Anyway, the strings are made of steel while saddles are brass, a softer metal, and I can see how they marked the saddle (you can even see string winding marks transversal to the groove!).
The proper solution would obviously be buying new blank saddle to substitute the old buzzing one but I met a repair guy who melted some soldering wire that filled the string winding mark gaps for free and that was it, problem solved for now. He said the material would partialy fuse to the brass saddle so it will not peel off or something, but I believe they can be pressed and deformed again during the coming years. If so, its not a definitive solution but I can live with that if I have to do it again only in far future.
