I'm having a weird problem. Using Xilinx Zynq board, I program the FPGA with bitfile included in my BOOT.bin. The FSBL programs my FPGA and linux boots up. I start my application. But some aspects of the FPGA like some FIFOs, interrupts do not work at this point. Some FIFOs are functional and work as expected. The weird part is that, if I program the FPGA manually by typing in "cat /path/to/bit.bin > /dev/xdevcfg " on the linux, everything works fine.
The same issue of partially programmed FPGA is observed if I put "cat /path/to/bit.bin > /dev/xdevcfg " in rc.local file. Not able to figure out if it is a FPGA issue or linux issue. Any help would be appreciated. Thanks.