I also posted my problem in the Xilinx forums (http://forums.xilinx.com/t5/Embedded-Linux/Zynq-FSBL-cannot-read-BOOT-bin-from-SD-card/m-p/522631/highlight/false), but as they couldn't help me yet and it also might be a MicroZed related problem, I'm posting it here now as well.
I have a MicroZed board with a Zynq 7020. I created a Project in Vivado and applied the board definition files provided here: http://zedboard.org/support/documentation/1519. Then I created a FSBL project in the SDK based on that hardware project. As a minimal example I generated a bootimage using the FSBL I generated and the u-boot.elf from the SD card image provided by Avnet, from the same link as above. I enabled the debug output of the FSBL and it tells me this:
Xilinx First Stage Boot Loader
Release 2014.2 Sep 22 2014-14:34:28
Devcfg driver initialized
Silicon Version 3.1
Boot mode is SD
SD: rc= 0
SD: Unable to open file BOOT.BIN: 3
FSBL Status = 0xA009
This Boot Mode Doesn't Support Fallback
In FsblHookFallback function
I am able to boot from the original BOOT.bin provided by Avnet, so neither my SD card, nor my MicroZed should be broken. As suggested in related threads, I also verified that the CD and WP pins are configured right and that the SD card clock is set to 50MHz. I tried routing the WP pin to an EMIO without any success. I also tried it with and without a .bit file. Is there anything else I could try?