I had similar problems with getting my second SD card to work when I first hooked it up. I do want to say up front that I am not using the SD card socket on the panel due as it was not in a convenient location given the way I ended up designing the enclosure for my Lcd, I have a external SD card slot breakout board. Nevertheless I do think what I did may help. From my looking into this issue this most recent go around and with my last 3d printer where I had similar issues, I found that the problem was ribbon cable length. It wasn't so much that it was too long, its was more about it being the correct length in the range of the length I needed for my application. From what I have read online it's something along the lines of signal reflection or something like that I think is was is happening. Both times I ended up shorting the cable by about 10mm and then it worked properly. If your are able to crimp ribbon cables give it a go and see if it works, you may need to shorten it a couple of times to get it working.
As a side note I saw an app note from a manufacturer, can't remember which one, that said for long length spi communications differental signaling should be used, the same type as rs422. That would require an active converter ic at each end of the cable, maybe some day I will get around to designing a board and try it out.