I have managed to find a work around, not very nice.. but as they say... someone with a little knowledge can be dangerous....
The probe logging started failing after a few minutes, but when I run:
/usr/bin/pineapple/site_survey 10
The probe requests start coming in again for another few minutes.
Added this script and to crontab and it runs every 15min kickstarting the probe logging.
Rebooted now and will monitor it.
UPDATE:
So found this in Logread, would it be related:
Aug 23 18:00:15 Pineapple daemon.info hostapd: wlan0: STA 70:8a:09:21:42:22 IEEE 802.11: authenticated
Aug 23 18:00:15 Pineapple daemon.info hostapd: wlan0: STA 70:8a:09:21:42:22 IEEE 802.11: associated (aid 1)
Aug 23 18:00:15 Pineapple daemon.info hostapd: wlan0: STA 70:8a:09:21:42:22 IEEE 802.11: disassociated
Aug 23 18:00:16 Pineapple daemon.info hostapd: wlan0: STA 70:8a:09:21:42:22 IEEE 802.11: deauthenticated due to inactivity (timer DEAUTH/REMOVE)
Aug 23 18:00:15 Pineapple daemon.info hostapd: wlan0: STA 70:8a:09:21:42:22 IEEE 802.11: authenticated
Aug 23 18:00:15 Pineapple daemon.info hostapd: wlan0: STA 70:8a:09:21:42:22 IEEE 802.11: associated (aid 1)
Aug 23 18:00:15 Pineapple daemon.info hostapd: wlan0: STA 70:8a:09:21:42:22 IEEE 802.11: disassociated
Aug 23 18:00:16 Pineapple daemon.info hostapd: wlan0: STA 70:8a:09:21:42:22 IEEE 802.11: deauthenticated due to inactivity (timer DEAUTH/REMOVE)