just received my first wooden flute 
on it, i must say, i tend to blow my middle Ds way sharp to my ear, and my low D’s quite flat, just curious how this may occur, since i simply lift L1 to go up the next octave, without much change to my embouchure, which i assume would be the main thing affecting pitch (?. i don’t have the same problem for my tipple, though. i hear of low Ds tending to be blown flat, but i seldom hear of this problem together with a sharp middle D, thoughts anyone?
What happens if you play middle D with xxx xxx?
hmm, the pitch may have lowered a tiny bit but i don’t really hear much of a difference
Of course I don’t know what kind of flute you have, but on my homemade flute I have the same problem. It is a D foot model. (So no extra unfigered / keyed holes below the bottom D.) After inquiry on this forum, it turned out that this design requires a much greater bore flare than I had expected from looking at a C foot design. Maybe your (anonymous?) maker stumbled over the same issue?
Then again, I don’t want to worry you; it may be that this new flute requires a different approach than your Tipple. For instance, I can correct a large part of the problem by turning the flute inwards on the lower notes. (Which is not to say that I don’t want to re-make the foot section next season.) On another flute the scale was completely off initially, but now I got used to it; this one had to be played completely turned outwards.
It may not be a first sign of quality if you have to make these kind of arrangements, but they can certainly help making your flute useable.
i play a burns folk flute. yeah, perhaps it requires a totally different approach than my tipple, everything about these two flutes are different, wood vs pvc, conical vs cylindrical, small holes vs large holes, oval embouchure vs round embouchure. and probably as a consequence of this, my embouchure causes a different set of intonation issues, on the tipple i tend to be sharp on the high B, A, and G, while i’m generally in tune (or just a tiny bit flat) on the burns. middle and low D are quite spot on for the tipple, for me, but sharp/flat on the folk flute. and i find the higher octave easier to reach, somehow, with the folk flute, but it requires a little more concentration on the tipple
Strongly suggest you to write to Casey.
so i’ve been experimenting with different angles of blowing the air stream, different degrees of how much i cover the embouchure hole, and it turns out, it alters the pitch much more dramatically than i’m used to. and i can bring the pitch down on the middle D by rolling in (if i play sllllooowwwly). though to do it while playing at a reasonable pace is beyond me for now. its very subtle, i find, the changes i have to make, so right now its a hit and miss. that’s something i’ll need to develop over time.
I’d suggest that you play the Burns long enough to get used to it.
No two flutes are the same.
However, some are farther apart than others. 
Casey’s and Doug’s are both fine flutes but they share little in the way of personalities.