Hi goose,
If you are talking about the script that has a demo on article on this site Kodyaz
How to Auto Format And Mask Telephone Numbers with Javascript, then this script is not throwing the cursor to the end of the entered string in the textbox.
I think, it was as you have written in the earlier versions, but if you make test on the textbox you will see that the cursor stays where you have added or updated new digits into the phone number.
I do not know you may be write on browsers other than IE.