Try going to the admin section
under define orders & order sets,
You can change the CPT code ALONG with whether it is auto added
I believe it WILL add the code.
(Actually I think I got this from YOU from this prior post
( http://amazingcharts.com/ub/ubbthreads.php/ubb/showflat/Number/63298/Searchpage/1/Main/6891/Words/vaccine/Search/true/Re:_Vaccine_Codes_Automaticall#Post63298 ) so I'm guessing you already tried this.
Another spot to reset would be admin, misc preferences to auto add admin codes
Perhaps the preferences were scrambled somehow and need to be reset