That's a real bummer and kind of inexcusable for a new guitar. Surely, Guild will want to make it right.
Usually a neck that needs a reset will manifest as uncomfortable action and poor intonation because you're having to stretch the strings to get them in contact with the frets up the neck. However, on a new instrument, the neck angle could be over-set, that is to say, tipped back too far. This is sometimes done , especially on 12-strings, to give a little room for geometry changes that you can expect to happen over time. If you laid a straight edge along the frets of an over-set neck, the end would align above the edge of the bridge, somewhere along the height of the saddle. Now, this kind of neck misalignment could very well cause the type of dead spots that were described. Also, this kind of neck misalignment, unlike the other kind, would be more likely on a newer than an older guitar. Whether a neck should be over-set is controversial. I've heard luthiers disparage this practice. It's predicated on the idea that the geometry can't be built to remain stable, which doesn't seem like it should be the case. Furthermore, even builders who might endorse this practice would agree that any over-set should be very subtle and certainly not so extreme as to cause problems with fretting the strings. As we have discussed in another thread, saddle height from the factory is usually intentionally at or near the high end, with the expectation that it will be lowered to suit the buyer. A neck angle that can't accommodate that adjustment without leading to the type of problem described is a bum job, period.
As I said, I suspect (and hope) that Guild will acknowledge this issue and put it right. If the neck is finished separately from the body, a neck reset shouldn't be too big a deal, especially in the Nashville shop. If the neck and body are finished as a unit, getting the neck off neatly and getting the neck/body seam to look right will be a little bit trickier and the extra drying time for the finish touch-up will slow things down a little bit, but not much.
Getting this done, and done now, is definitely the way to go. It'll be a bummer to be without the guitar for a while but when everything is put right, it'll be a closed issue and you'll just be able to enjoy that wonderful guitar with no worries. Hope it goes quickly and smoothly.