This bothered me for the longest time...
Don't re-center, as you'll lose your target half the time. Just do this- rather than fight it, try working with it, in the direction it's moving. IE, if it starts scanning left, hit the left directional input and it will stop. It's counterintuitive, which is why it took me so long to figure this out for myself.
The command seems to "stick" sometimes and the only way to clear it is to re-input the same command... fighting it doesn't do anything. It's kind of annoying, but you'll stop noticing it and do it automatically eventually. I generally only have to do it once per mission anyway...
PS- are you using a Saitek?