How to stop itunes from popping up?
When plugging in a Apple device such as a Iphone / Ipad / Ipod?
To Fix
You must Disable this Feature in iTunes,
But sometimes you need to plug your device into another computer to charge its battery. In that circumstance, how do you prevent the warning or data mistakes?
Easy – disable auto-syncing. Here’s how:
1. Before you plug the iPhone or iPod into the computer, go to iTunes.
2. On a Mac, go to the iTunes menu -> Preferences -> Devices.
On a PC, go to Edit -> Settings -> Devices
3. In the pop up window, look for the icon or tab that says Devices. Choose it.
4. Just below the box, you’ll see a checkbox reading “Prevent iPods, iPhones, and iPads from syncing automatically.”
5. Check it and click OK at the bottom of the window.
Auto-sync is now turned off and you’re safe to plug your iPod or iPhone into the computer.
Also Check the Summary of the Device when it’s plugged depending on the verison of itunes it might also be located there.
It’s randomly popping up while on internet or on desktop?
To Fix 
1. I would recommend you to run iTunes as administrator.
Perform the following steps on all the iTune related shortcuts.
1. Right click on Itunes icon, then click Properties.
2. Browse to the Compatibility tab and under the Privilege level place a check mark on “Run this program as an administrator”.
The above procedure have resolved both the issues, popup and Live Messenger.