I appear to be experiencing the same issue that user "zoro25" opened a ticket for on 1/27/2016 found here: https://www.wifipineapple.com/bugs/378
Recon mode is only seeing two or three of the dozen SSID's I know to be broadcasting at any given time in and around my apartment building. PineAP does not collect any SSID's at all, except for the network that my phone is on which is tethered to the NANO. When I first purchased this unit, there were no issues in Recon or PineAP, both worked as advertised and flawlessly. This issue was first noticed immediately after upgrading to the 1.0.4 firmware. A further upgrade to 1.0.5 has not rectified this issue, nor has resetting the device to factory through the GUI, or through a long hold of the reset button.
Please note that my Pineapple Mark 5 has no trouble seeing the networks when using it's recon mode, nor does it have trouble collecting SSID's using PineAP.
I am a huge fan of Hak5 and its products, using them in my everyday work. Please help me to address this most frustrating bug, as it has essentially rendered my most recent purchase useless.
I must admit that I am somewhat perplexed and frustrated at the total lack of response from the hak5 dev team regarding this issue. Considering it has practically rendered my device useless I would assume that some kind of proposed solution would have been made by now, even if that proposal was to offer me a new device (which it appears at least ONE other customer was offered...)
I suppose I will just have to continue waiting and hoping that my early buy-in of the NANO was not a mistake.