Question: Whenever I fire a weapon or stomp, my computer emits the new device sound and disables my controller for a split second, meaning I fire a shot or two on an automatic rifle and then return to stance. This only happens with stomp or shooting while zoomed in. It doesn't happen with running, or striking.  

Any ideas?

Answer: 
You might be running into one of the issues mentioned in this article:
<http://kotaku.com/wanna-catch-your-pokemon-in-a-shiny-new-color-in-x-y-1450801224>

For instance, you could be walking into Slow or Normal shaking grass, which could be breaking your chain.
There can be several possible causes for this:

1. Leaving the field you were chaining in.
2. Turning off your game.
3. Using any other key item besides the PokeRadar.
4. Having an egg hatched during your chaining.
5. Running into a wild Pokemon that is not from the PokeRadar. You can use Repels to avoid this.
6. Stepping into a grass patch that is on the border of the grass area. It apparently almost always breaks your chain, unless you reset (use again) the PokeRadar.
7. Stepping into a grass patch which is shaking next to another shaking one. This apparently can break your chain as well.
8. Stepping into a grass patch which shakes differently from the one you were chaining. If that grass patch barely shook, you'll get the message "It seems there is no Pokemon here". It's sometimes difficult to spot those, especially if its behind the head of your character, or behind some obstruction.
9. Stepping into patches that are less than 4 steps away from your original position apparently can break your chain as they tend to hide different Pokemon than the one you're chaining. If you don't have any patch of grass at least 4 steps away,walk 50 steps making sure not to step into any shaking grass (even those which barely shake as these will break your chain as per point 8).

Taken from [here](http://www.reddit.com/r/pokemon/comments/1ot6ex/chaining_tutorial/) and extracted/summarised the relevant parts.