[U-Boot-Users] lowlevel init and reboot issue

Hello,
I am running a board similar to the at91rm9200ek board. It has been stripped down of few peripherials for minimal power consumption purpose. I am running uboot 1.1.4 and linux 2.6.16. U boot loads directly from parallel flash into ram.
My problem is that I cannot restart the chip from linux. I followed the watchdog code, and it does execute. Linux also closes up fine. However, the processor does not reset at the end. The weird thing is that a reset works fine from uboot. The code is almost identical between the uboot reset and the linux system call. Both set the reset pin and make a watchdog overflow.
I believe that my issue lies in a uboot setting somewhere in the initial linux setup. If I load ubott 1.1.4 without low level init by means of yet another loader loading uboot from flash to ram, the reset runs but very slow. However, my uboot utilizes the lowlevel init. Somehow it affects my watchdog timer and stops me from resetting the chip.
Has anyone run into this issue? What could be stopping me from resetting?
I thought that the watchdog timer was a purely hardware tool. I thought that setting and overflowing the timer would reset the chip on a hardware level. Please help. I have spent a week or so on this and cannot figure out the issue. It is probably very simple and is my oversight, however, I cannot see it yet.
Thanks again, Roman
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Roman Kolesnikov