My first ever Pineapple that arrived today was suffered from the same issue. The SD card worked fine in my Linux machine and the MD5 values matched.
I worked out that the SD card shipped was formatted in EXT3/4 which my Pineapple wasn't picking up and hence the continuous amber flashing lights. I formatted the SD card in FAT32, transferred the most recent firmware from https://wifipineapple.com/?downloads onto the card (as the original on the SD card also out of date) and now it works as expected.
I am really glad because I wasn't looking forward to doing a RMA back over the Pacific.
