I'm not sure your doing it right..
1) Download the "stager.bin" and "upgrade.zip"
2) With the WiFi pineapple off put the DIP switches in up, up, up, up, down (1 1 1 1 0)
3) Connect the Ethernet to WiFi pineapple and computer, then assign the computer a static of 192.168.1.2
4) Plug the WiFi pineapple to power wait a min then nav to 192.168.1.1 on the web browser.
5) Give the recovery the "stager.bin" wait till its done then and say to turn off.
6) Extract the "upgrade.bin" form the zip file. in to the SD card. (now make sure you reformat the SD to FAT (not FAT 32) and put the upgrade.bin and md5 file in the root of the SD.
7) With the WiFi pineapple off Put the DIP Switches back to up, up, up, up, up (1 1 1 1 1) and put in the SD card.
8) Power the WiFi pineapple with the AC adapter and wait till you see the Set up order of the LED's
Green means power
Solid Blue mean it in the process of Flashing.
Amber will blink meaning the it's looking for the upgrade.bin file.
Then if you don't get the Red LED (Red Solid means didn't match MD5)
Then the Blue LED should start blinking meaning the WiFi Pineapple is Booting up.