Well I checked everything suggested as far as I know. I bypassed the power switching pin, putting 5v straight to the vcc pin on the reader. I checked the regulator, solid 3.3 out. I tried various sd cards. I'm out of ideas. The only spi device is the sd reader so that shouldnt be the problem. I noticed at one point the atmel chip was pretty hot, not hot enough to burn me but still hot. That problem went away and I still don't know what caused it. I have a few of these pro-minis so I guess I'll try swapping it out. Wish I hadn't already hot glued it into its enclosure. If that doesn't fix it got any ideas? What sd reader would you suggest in place of the one I have?
Thanks again