As of Delek's new prerelease of Deflemask 12.1, wave phasing appears to work! At least better than it did before! you still get the default minor HuC6280 pop once in a while, but NOTHING like it was before.
Also (and this is a biggie) the bug where you switch from notes to samples and you're samples are locked at 1 volume is gone! now i'm free to switch a channel from one to the other at my leisure. YAY!
This new version is pretty good, but you missed the pre-release of version 12.0.0 mate, that one was the best! It used its own custom window for opening instruments and wavetables, you could easily 1-click the wave you wanted and test it on-the-fly without closing the window, and when you found the wave you wanted you could just select it and be done...
Since version 12.0.1 they've changed it to the traditional Windows "Open File" window, and it sucks, you have to select the wave and the instrument you want before you can test it, so every time you want to load a new wave you have to click "Load Wave" then select your wave and click "Open" and THEN test it, and if it isn't the wave you wanted you have to do it again, and again, and again, until you find the wave you want... Yeah I know that I'm supposed to remember what each instrument sounds like based only on their file names, but I'm too lazy for that, and the old window was SO much faster and more convenient! I wish they'd bring it back...
Thankfully I haven't deleted my favourite old version of the tracker, so I can easily make my songs on that version and just open it up on the new version whenever I need to export a .hes file, that said though, with Huzak existing and all it's gonna be kinda pointless to even use Deflemask's .hes export, thus rendering any new version of the tracker that doesn't contain the PC engine CD add-on or the noise mode envelope pointless to me...