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Maybe some of the information at https://unix.stackexchange.com/questions/113939/wpa-supplicant-overriding-iwconfig can point us in the right direction?

Someone on there posted-

I fixed this by adding nohook wpa_supplicant to my dhcpcd config file, and changing my "connect" script to only invoke wpa-supplicant for wpa networks.

sudo iwconfig "$INTERFACE" essid "$SSID" key "$PSK" 2>/dev/null
WPA=$(printf "$TABLE" | grep "$SSID" | cut -s -d $'\t' -f 2- | grep "WPA")
if [[ $WPA ]]; then
sudo wpa_supplicant -B -D wext -i "$INTERFACE" -c "$WPA_SUPPLICANT_CONFIGURATION_FILE"`
fi
sudo dhcpcd "$INTERFACE"