Im really not sure about that issue as I've not encounted it myself, the only processes that are killed are:
NetworkManager
wpa_supplicant
The only other thing in the attack mode section is macchanging.
I don't have that issue and I can't get access to another machine for a while so I can't really look into it to well, hopefully someone else might be able enlighten us.
Cheers for the suggestions.
I haven't looked into mdk3 properly yet, will have to try the attacks myself and see how I can impliment them into the script (More headache!! LOL).
Oh I just had a thought, maybe the timing might be out, you could try making the sleep time longer.