Wiecheng,
Unfortunately I don't know this board in details but, if possible, I would check the voltages of the multiple VDD rails and see if they are within the device spec. The board may have test points for that, since probing pins on a high density BGA is far from trivial (if not impossible).
In my opinion, if the manufacturer lists the board voltage tolerances it is probably safe to operate with the higher 3.3V supply. I would also check if the power adapter is able to supply the maximum current used by the board (especially at power up, where it can suffer the largest surge) and verify if its ripple/noise ratings under load are acceptable.
You already mentioned you are using a voltage translator for your XDS510USB, therefore it shouldn't be a problem (this particular emulator is not specified for operation under 3.3V)
I am not sure what else I could help in this case, as it seems extremely hardware related and unfortunately I don't have the same board as yours. In any case, give these suggestions a try and see if you can get some additional insights about what may be happening.
Hope this helps,
Rafael