ITunes backup app

I've updated to latest version of iTunes and iPhone software. Keep getting a 'Choose application' window flashing up saying 'Where is iTunes Backup .app'. There doesn't seem to be any great consistency to when this happens, and iTunes isn't always running when it does happen. Anyone able to help on what this is about?

Ok I understand all that, so the iTunes needs to save the apps and the iTunes backup saves the app data.
so I'm plugging my iPhone in, selecting backup with iTunes as that's what I want, I also want it to save apps where I have them and everything.
so I'm selecting my phone going over to Apps as ticking sync, this is telling me this "are you sure you want to sync apps? All existing apps and their data in the jog know will be replaced with apps from this iTunes library"
Is that going to delete my apps from my phone? I don't have a single app on the computer.
I want it to copy the my apps from my phone to the PC and the app data in the backup.
Sorry for being a bit dumb here
Thanks :)

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