I also have a Transformer and had exactly the same issue. I have had 2 and both experienced the same rebooting loop problem (the first also had a problem with the dock not charging). I experienced the same issue with both Android 3.1 and 3.2. Given the number of people reporting this issue in various forums I suspect it is software related rather than hardware.
Originally I did not have any security set up on the device. However since I added a security pattern to unlock the device I have not had a single issue with the device rebooting. I would be interested to know if this fixes the issue for other people too.