Hi Othannen,
It sounds to me that you have made your flute from extruded PVC piping? If so, and it has a totally cylindrical bore, it doesn't matter how careful and clever you have been with the finger holes, embouchure cut or stopper placement and seal, it may have a good tone, but it won't play in tune "over the break" into the second octave unless the bore diameter is exactly in the right proportion to the length of the flute, as with some bamboo flutes and the Renaissance flute. That is unlikely working with pipe like Electrical Conduit Piping etc. and making a standard D flute. It will almost certainly play flat in the lower part if not the whole of the second octave, although you may well be able to "lip it in", which is a major problem when test tuning as you cut and adjust tone-holes! You can quite easily make a simple cylindrical flute that will have a strong and beautiful tone and play an in-tune scale of a seventh, from the bottom D up to open C#. After that, problems!!!!!!
I learnt all this the hard way some years ago, and that was with the benefit of having read Boehm's
Treatise and various other works on flute acoustics and historic development - although I can't claim to have taken a scientific approach, just that I understood the theoretical problems. I strongly suggest that, instead of wasting time and effort and much heartache experimenting yourself, covering ground that much has been written about, that you read up on the issues. A good place to start is Doug Tipple's website (I'm assuming you aren't familiar with it - sorry if you are!) - he even has a solution to the bore-properties problem - the
Tipple-Fajardo Wedge.
The fact that there are some makers of flutes in this type of material who are selling simple, basic cylindrical flutes does not mean that they have solved fundamental difficulties with the physics/acoustics of flute tubes. Very clever placement and sizing of tone-holes combined with a fairly small embouchure hole (which limits the strength of tone) can permit a (barely) tolerable tuning of the scale over 2 octaves, but such things, e.g. the Dixon ones, are not satisfactory beyond the "trying it out" beginners stage because the intonation problems are still there, just minimised.
The bottom line is that if you want a decently in-tune flute, you must either have a cylindrical head with a tapering conoid body, or a cylindrical body with a Boehm type "parabolic" reverse-tapering head. (The wedge mentioned above partially simulates this effect). In extruded tube, neither of these alternatives is easily achievable.
If your experiment is not making the sound you want, it will not be due to the material (although subjectively at least, most people do feel that materials make subtle differences, even if science suggests they are wrong!) but chiefly to the dimensions and cut of your embouchure - assuming that your original question was about the kind of tone it makes rather than the tuning of the scale. When you get the tone, you will still have the tuning problem.
Here's a
link to Doug Tipple's website. You may find the "Flute Player's Guide" page a good place to start. It includes a discussion of the "Materials Question" too.
It is possible that your end stopper/cork even when it doesn't leak may be another source of problems, in that its placement is important both to intonation (tuning) and tone production.
You are quite right that working in wood (or solid forms of plastic) requires special tools and skills - lathes etc. The English word for making the hole through the material for the bore would probably be "hollowing it out" in lay terms: in technical terms, it is drilled and reamed.
Good luck!
