Updated Iphone 4 and Itunes 11.. cannot update checked music and apps

Computer uses Windows 7. 
Iphone is a version 4 with IOS 6.0.1 loaded. 
Itunes is the latest version of 11.
I noticed my new Ipad mini has no issue with connecting to Itunes and it does read what apps I want removed and added.
The Iphone 4 however is having issues.  I notice that Itunes locks up a lot which could possibly be an issue with the computer but unclear.
I have certain songs checked..when going into the music section prior to connecting the phone.
When the phone is connected I can see the settings for the phone and in the general part I have tried different configurations.. I tried sync checked audio and video only...I have redone it with checking manually control of music/video. 
I noticed based on which of those two are checked it will either check or uncheck the actual sync box in the music tab for the phone.  If in the music tab of the phone that is checked....it gives me different things to click like "Band" or "Album" and still disregards any selection I make there and will not change the present music in the phone.
My issue is overall it completely disregarding the audio selections and keeping whatever audio is on the phone where its at.  It will not add the new CDs I purchased to the phone even though they are checked in Itunes.  The apps are not updating either...In the phones app tab it says it will remove apps but does not and will not add other either.
Version 10.7 seemed to be glitchy for me as well...it seemed I had to do 2 syncs to get it to accept my choices but would accept them.
Am I missing a setting?

After upgrading i06 on iphone 4 and Itunes 11 on pc
Does anyone know how to solve why the apps sync starts installing apps on the IPhone, blue bar gets to mid point for each app (even 1 app) then hangs i.e. fully clears the blue bar as if it hasn't started. Occurs on cable connection and Wifi sync.
This then stops you from installing any apps as the hung app shows installing but not doing anything.
Installing new apps is fine however.
cheers

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