Reasons for fly not sitting right;
1. Poorly tied fly; if the materials are unbalanced, and the fly lists to one side, this could be a problem. Fly should be balanced and symmetrical. There's nothing you can do to solve this issue if you have a poorly tied fly.
2. As the above poster suggested, hackles can be an issue. Related to #1, poorly wound hackle can be a problem. Parachute hackles do tend to sit nicer in the water. Solution is to switch to parachutes, or, ensure when you buy or tie vertical hackle flies, make sure they are evenly wound. Also, Don't buy or tie overly hackled flies. Yes, the western N.America style is to use Wulff style flies for our "rough" water, but some flies are just crammed with 6+ turns of hackle. Crazy!
3. Poor cast; are you slapping the water or letting the fly land gently? Fix the presentation cast; aim above the water, let the fly settle.
4. Foam patterns; many foam patterns extend the foam body right over the eye of the hook. The fly can often land upside down. The only solution I've found is to really work the materials back with your thumb, try to create some clearance between the hook eye, tippet material, and the interfering part of the of the foam.
5. Knot placement. Related to helping #4, take the time when you tighten your knot, make sure the knot rests in a neutral position on the hook eye and/or slightly upward (slightly upward for foam patterns for sure). Knot position is often overlooked.
6. Tippet length and strength. Long a tippet will help mitigate drag (including micro drag), but having it too long diminishes that effect and increases your odds of the fly landing improperly. I don't see many situations that require more than 3 feet of tippet. Also related is the strength/diameter of the tippet and how supple the material is. Balance those out.
That's all I can think of. Often, when I get a fly that simply won't land properly, I'll often try changing the knot position and adjust the casting. But after a few attempts, I'll just switch the fly. I want to fish, not get into a CSI investigation of why my fly isn't performing properly.
Smitty