I also experienced problems, including this one.
I upgraded a firmware 1.02 router directly to 1.21 B04. It had many errors in the admin web interface, the left menu was full of options outside of their respective sections. I solved this reflashing 1.21 B04.
Some minutes later I flashed to 1.21 B05, and configured the router to act as a switch (I have another DIR-655 at home used as my main router). A couple of hours later, I decided to enable the wireless radio on the secondary router, so it acted as a switch + AP. But the router rebooted every time I tried to save the settings, without saving them. I solved it by reseting the unit (pressing the little button on its back)
As of now, it seems to work well, it saves my changes correctly and offers to reboot when needed.