AdsGone v4.2.4 or newer has a checkbox on the ad blocking tab that allows you to enable or disable "Messenger Service" which is what's causing those types of popups.

1) Use the checkbox or

2) The following is how to manually enable/disable the service:

This is how to disable the Messenger Service

To remove the ability for anyone in the world to pop up messages on your computer, you can disable the Messenger service. Its easy to reverse at a later time if you wish to do so.

 
 
Windows 2000
Click Start-> Settings-> Control Panel-> Administrative Tools->Services
Scroll down and highlight "Messenger"
Right-click the highlighted line and choose Properties.
Click the STOP button.
Select Disable or Manual in the Startup Type scroll bar
Click OK
 
 
Windows XP Home
Click Start->Settings ->Control Panel
Click Performance and Maintenance
Click Administrative Tools
Double click Services Scroll
down and highlight "Messenger"
Right-click the highlighted line and choose Properties.
Click the STOP button.
Select Disable or Manual in the Startup Type scroll bar
Click OK
 
 
Windows XP Professional
Click Start->Settings ->Control Panel
Click Administrative Tools
Click Services
Double click Services Scroll
down and highlight "Messenger"
Right-click the highlighted line and choose Properties.
Click the STOP button.
Select Disable or Manual in the Startup Type scroll bar
Click OK
 
 
Windows NT
Click Start ->Control Panel
Double Click Administrative Tools
Select Services-> Double-click on Messenger
In the Messenger Properties window, select Stop,
Then choose Disable as the Startup Type
Click OK
 
Windows 98 & ME
Windows Messenger Service cannot be disabled because it isn't part of the OS (you should not be able to get Messenger Service Popups)