If you're describing what I think you are, that's the other thing I started to mention earlier, and thought you had found the bridge saddle to be the culprit, so I dropped it.
I've seen this a few times, it was the main problem with my Takamine. I didn't spot it before I bought the thing, I would have left it on the rack if I had. I don't know why, but some acoustic necks drop away from the body. If you sight down it from the bridge end it's easier to see, it looks like a slight hump right where the neck joins the body. That's what I've been dealing with on mine. It's visible on both sides of the neck, and mine is not twisted. I think I finally have it beat, but still might need to do a little more work on it. The only way I know of is to file down just those last few frets to give it more clearance, or raise the bridge until it's unplayable. I've filed the frets 3 or 4 times, trying to go just a little and create clearance, the bottom 3 strings start to buzz against the frets at about the 8th or 10th fret. Then it just goes dead. That hump is a bear to deal with. Truss rod won't adjust it out, it has very little affect at the body joint area, although it did help a little, and it needed less back bow to begin with. (way too much first time I checked it) It sounds and plays absolutely great, so I haven't given up on it yet, but it's been an ordeal trying to repair it.
The actual option here to really fix it, would be send it in and have the neck replaced...with another made out of the same green wood that dried and dropped here most likely...and would cost half the price of the guitar, (I got it for just under half its original $800 price tag) so I decided on filing the frets to create some string clearance and keep playing it. I think the humidity around here actually helped it, almost 10 years of wet Louisiana winters has helped make it better, and parking it leaned against the wall, which I never do, helped a little too. It plays great and sounds fantastic, as long as I'm real careful around that part of the neck. Pick the G or B string a bit too hard and it buzzes...Next string change it gets another light filing job...
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