I had the same problem. I'm running BE10 rev5520 sp1. After I installed the Service Pack, the auto reply to Media Remove alerts no longer worked. I tried everything descrbed in the two KB articles, but nothing worked.
I had it set to Respond Yes after 5 minutes, and they were being responded to by ADAMM with response None every 7 minutes for days and days (if I didn't manually click OK).
I changed the response time to every 1 minute, and it seemed fixed. I just checked my Alert History, and apparently they are still being responded to by ADAMM with response None, but now it's every 3 minutes and eventually (after 3-4 hours) the System responds Yes.
So I guess it's not totally fixed, but they are being automatically responded to before work the next day.
I don't know if this will work for you. Good luck.