End user notifications not appearing for Software updates

I'm pushing out security updates to Windows 7 clients. The updates are deploying correctly but some users say they are not seeing any notification that the updates are available or that they are installing - It's set up in the deployment to notify. They
say the first time they know about them is when the machine reboots. On my own machine I always get the notifications, on all the IT users near me we always get the notifications, and on all the test machines I've built I see the notifications. It's possible
my users are just not registering the message before it fades away.
I've made some changes to the Computer Agent, Greater than 24 hours - remind every 3 hours, less than 24 remind every 2 and less than 1 remind every 5 minutes so that may help. What I'm wondering though is there a local log on the client end anywhere that
updates every time a notification appears - I could at least verify it - or is there a local reason why the balloon doesn't show. It's not turned of in a GPO.
Is there any way that the balloon can be replaced with a pop up that the user would have to click OK to clear?

Thanks for the reply - I had a look at the logs - here's an example
Adding Open Software Center Menu for Icon Microsoft.SoftwareCenter.Client.Notification.NotifyObjectComplete, because no required item and no reboot are present.      (Microsoft.SoftwareCenter.Client.Notification.NotifyObjectComplete at get_VisibleMenuItems)  
 SCClient    05/11/2014 12:15:55    1 (0x0001)
Setting the current app data      (Microsoft.SoftwareCenter.Client.Notification.NotifyObjectBase at HandleNotificationEvent)    SCClient    05/11/2014 12:15:55    1 (0x0001)
Verbosity set to low, don't show balloon      (Microsoft.SoftwareCenter.Client.Notification.NotifyObjectBase at HandleNotificationEvent)    SCClient    05/11/2014 12:15:55    1 (0x0001)
The current visible object is of type Microsoft.SoftwareCenter.Client.Notification.NotifyObjectInstalling with priority Installing      (Microsoft.SoftwareCenter.Client.Notification.NotifyObjectBase at HandleCurrentNotifyObject)    SCClient  
 05/11/2014 12:15:55    1 (0x0001)
This object is of type Microsoft.SoftwareCenter.Client.Notification.NotifyObjectComplete with priority Completed      (Microsoft.SoftwareCenter.Client.Notification.NotifyObjectBase at HandleCurrentNotifyObject)    SCClient  
 05/11/2014 12:15:55    1 (0x0001)
Removing monitored notification object Microsoft.SoftwareCenter.Client.Notification.NotifyObjectInstalling for app Security Update for Microsoft .NET Framework 3.5.1 on Windows 7 and Windows Server 2008 R2 SP1 for x64-based Systems (KB2972100)   
  (Microsoft.SoftwareCenter.Client.Notification.MonitoredNotifyObjectsCollection at RemoveObject)    SCClient    05/11/2014 12:15:55    1 (0x0001)
Number of total seconds in countdown is 5400; starting value is 4; seconds til restart is 5396, system will restart at 13:45:54 (utc end time = 13:45:55)      (Microsoft.SoftwareCenter.Client.Pages.RestartCountdownDialog at .ctor)  
 SCClient    05/11/2014 12:15:58    1 (0x0001)
User will be alerted (and hide/close disabled) at 13:15:54      (Microsoft.SoftwareCenter.Client.Pages.RestartCountdownDialog at .ctor)    SCClient    05/11/2014 12:15:58    1 (0x0001)
ShowBalloonTip: determining if tooltip should be shown for notification type = Microsoft.SoftwareCenter.Client.Notification.NotifyObjectRestartCountdown      (Microsoft.SoftwareCenter.Client.Notification.NotifyObjectBase at ShowBalloonTip)  
 SCClient    05/11/2014 12:15:58    1 (0x0001)
Notification is for a logoff/restart required or logoff/restart countdown.      (Microsoft.SoftwareCenter.Client.Notification.NotifyObjectBase at ShowBalloonTip)    SCClient    05/11/2014 12:15:58  
 1 (0x0001)
Attempting to display the notification balloon with title 'Restart Required' and tooltip 'Recently installed software requires your computer to restart in 90 minutes to complete the installation. No additional software can be installed until your computer has
restarted.  '.      (Microsoft.SoftwareCenter.Client.Notification.NotifyObjectBase at ShowBalloonTip)    SCClient    05/11/2014 12:15:58    1 (0x0001)
The operating system version is 6.1.7601.65536      (Microsoft.SoftwareCenter.Client.Notification.NotifyObjectBase at ShowBalloonTip)    SCClient    05/11/2014 12:15:58    1 (0x0001)
This is Windows 7 or earlier, showing notification balloon      (Microsoft.SoftwareCenter.Client.Notification.NotifyObjectBase at ShowBalloonTip)    SCClient    05/11/2014 12:15:58    1 (0x0001)
NamedTimer: Starting timer timeToAvoidDisplayingTheSameBalloon, interval = 120000, period = -1      (Microsoft.SoftwareCenter.Client.Common.NamedTimer at .ctor)    SCClient    05/11/2014 12:15:58    1
(0x0001)
NamedTimer: timeToAvoidDisplayingTheSameBalloon initial interval = 120 seconds, subsequent period = 0 seconds, overall due at 05/11/2014 12:17:58      (Microsoft.SoftwareCenter.Client.Common.NamedTimer at SetTimerInternals)    SCClient  
 05/11/2014 12:15:58    1 (0x0001)
Would that imply that it's set not to show the balloon - except on the reboot?
I had a look at the following policies using wbemtest 
DisplayNewProgramNotification
CCM_SoftwareDistributionClientConfig/DisplayNewProgramNotification
CCM_ClientAgentConfig/DisplayNewProgramNotification
and both are correct - DisplayNewProgramNotification set to true

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