A couple things helped me. First, always make sure the logo on the ball is facing the SkyTrak. A flat/straight line logo works best (i.e., the Nike swoosh may not be the best choice). I've also had issues when my SkyTrak is not level, so I go into the SkyTrak app after I've moved the unit to make sure it's level, then exit out and open up TGC after a system reboot for good measure. I've also had issues when the SkyTrak is not level with or just below the level of my golf mat. I'm using a third party protective metal case, and if the unit gets even slightly higher than my mat, I have trouble. I've heard it's best to keep the SkyTrak off the hitting mat to avoid vibration, which can also cause reading issues. And finally, I switched from rubber tees to wooden tees and then finally recently to the Tomahawk Neo Golf Tees. The rubber ones were very durable, but caused a high percentage of mis and no reads. The regular wooden tees attached to a low profile plastic holder I could twist into my mat were fine, but I had all kinds of broken tee fragments all over my room. The Neo tees on the other hand seem very flimsy, but have actually been incredibly durable. I've played at least 50 rounds with just one of them, had guests over, and haven't broken one yet, and haven't had any mis or no read problems.
Also, if you haven't checked out the Golf Simulator Forums (external site), that's an awesome place for suggestions, as well. Good luck, and have fun - TGC with SkyTrak is an awesome package!