The version showing in Add/Remove programs is the version of the installer and most likely shows up multiple times due to the differences in versions of the installer. You can remove the 1.0.0.0 version but leaving both as is will not affect the application.
As far as the alerts not firing properly, here are a few things to look at.
In Central Administration go to Timer Job Definitions on the Operations tab and make sure there it an Immediate Alerts on each of the web applications you have alerts set on and make sure they are not Disabled.
Also, create an alert using the basic SharePoint Alert Me alerts to see if these fire successfully. If so, then create the same alert using Alert Manager's Advanced Alert Me without using a custom alert template and see if these are successful. Immediately after creating these alerts, reset the Windows SharePoint Services Timer service.
If after checking all of these, contact us at softwaresupport@sharepointsolutions.com for further troubleshooting.