I have been trying to get SPI working so that I can use Flashrom to program a BIOS chip with Libreboot. I am using a Raspberry Pi Model B+ connected via short F-F jumper wires to a Pomona 5252 clip over the Macronix MX25L3205D chip on the motherboard. I am replicating a setup I successfully used to flash Libreboot to the same model of laptop (a ThinkPad T400) a few months ago, but something isn't working. My jumpers are connected properly for the pinout, the Pomona and chip are both making good contact and have been thoroughly cleaned with Isopropyl Alcohol, the jumper wires have been tested for continuity and resistance and there's nothing out of the ordinary with them, and spidev0.0, 0.1, and 1.0 are appearing in /dev. SPI is enabled in raspi-config, and I have set config.txt to enable the second SPI interface, just in case the problem I was having was with the first. Neither work. Flashrom reports that the chip cannot be found, while spidev-test (with MISO and MOSI bridged as specified) simply outputs its first three lines of information, before not outputting the table of hex values it is meant to. I have tried this on four versions of Rasbpian, the latest three (which span Debian 8 and Debian 9), as well as a version from 2014 which could not properly compile either of the tools I use to test due to package problems (I gave up on this version).
Just to be sure by B+ isn't dead, I have also tested this with a Model B Rev. 2, to the same results.
I think I must be misconfiguring something, somewhere on the Pi. I know this worked before, and I even flashed back the Raspbian version I used before for one of my tests, but I don't have the SD card I used then and I have no idea what could be wrong.
What is wrong with my SPI interface? This worked recently, so I think this should be fixable, but I am probably missing something.