did you ever look at the content of your page (source - fire bug or such a tool)?
You wold notice that some controls (depending on there position) change the IDs.
So a radGrid - becomes ctl00_radGrid or something like this.
I'm not sure if this is the fact in your scenario - but try to change your code to something like:
|aS.UpdatedControls.Add(new AjaxUpdatedControl(rgBackupFiles.ID, rajLoadingPanel.ID));
This is just code I copied from a running solution - of course you have to use your variables.
And your bulk adding is also OK - it's just about myVar.ID instead of "myVar".
I just saw you did the "id thing" in the constructor of you ajax setting - give it a try for the updated controls also.