I did a DONE4 in March through AA. My JNB-CPT segment was booked as CX7311 and I was given a CX boarding pass in SYD when I checked in for the SYD-HKG-JNB-CPT part of my trip. At JNB I was reissued a BA boarding pass as BA 6411 and was credited with only a 25% bonus versus 125% which I earned on all other CX segments. I have requested additional credit from AA twice with the last request about 3 weeks old.

Should I be entitled to the CX bonus since the flight was booked as CX even though it was a codeshare and the boarding pass was reissued in JNB as BA?

I flew CPT-xLHR-HEL last month using the AY code on the BA flight, had a boarding pass issued by BA at CPT with the BA flight no. on it but annotated "sold by Finnair" and got the full Plat bonus on the BA-operated flight.

I will say, however, that it took almost a month to post. I'd communicate again with AA and if need be fax them a copy of the ticket or PNR that showed the CX code on the flight. I assume is was part of a direct connection between HKG and CPT, and not after a stopover at JNB?

The best thing is to look at your itineary.
if it says cx then you should be credited regardless of the boarding pass. and you should send in your itineary along with the boarding pass when you request mileage. This is becasue the system has captured the ticket as BA instead of CX and requesting mileage now requires the proof of the itineary which orginally shows it as CX.

Actually these happen in some airports as the info screens only show example BA xx. instead of BA xx/CX xxxx. And since some flights got more than 1 codeshare, they cant list every flight.

The effiicient and smart airports will have the info screen show BA xx while on your boarding pass will show CX xxxx/BA xx, and someone else's might be AA xxxx/BA xx so the passenger who's not an idiot will look at the BA xx flight info on the info screens. But not all airports are "smart" that way.