I agree that it sounds like hardware not your mixing process (codicil: as long as you are using the right USP grades). The diluents used and the nicotine mix well and once they have been don't tend to settle out but I have not had that hold true with some flavors depending on what makes up the 'natural' part of the flavoring you use. Most artificial flavors are made in the same liquid consistently and are not heavy enough to settle out while a very thick or syrupy flavoring may. Make sure you are shaking before use not just when you mix it. Even if the flavor has settled a bit your 'symptoms' sound more like, as said above - a dry hit which is 'almost always' your hardware/settings. There is a slight possibility if the flavor you use has really thickened the mix it won't wick well and the device will give a dry hit - it which case you ultimately can blame the flavoring consistency not whether you shook enough or your hardware is causing it.
You probably are going to need to do some testing by varying your hardware devices and settings with a good idea of what the different devices and settings will give me in the way of taste, TH etc just because of the device itself. Dripping is a pretty good way of testing that you have mixed well although a vigorous shake should do it. I really don't like heat to help mix/steep e-juice but many swear buy it (you should read some posts on the best way to do it and pro and cons of what people think if you even consider it), but have done so with very thick flavoring to help is move easier and mix better. (heat does not thin it out because then you would have more flavor then you want diluting your base, it just means it moves around better to be mixed well.)
I would go the hardware route first before even considering possibility of other issues.