Hi Raghu, I've seen similar symptoms when on laptops when embedded controller (EC) interactions interfere. Delay loop calibration can be interfered if the EC is spamming the host chipset with SCIs (check dmesg output and see if the kernel complains about interrupt storms or some such). Also, if the EC and chipset BIOS share a SPI chip, then the EC might attempting to accessing the SPI chip at the same time and interfering.
You may need to consult your mainboard vendor and ask them if there is an "update mode" command you can use to prevent it from interfering with your SPI chip.
Also, your chipset might be configured to target the LPC bus instead of the SPI bus.
Please post the verbose output using the -V flag. You can paste it at http://paste.flashrom.org.
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David Hendricks