Sung,
I am not sure about the errrors you were seeing earlier, but the condition you mention is not a valid one for the TPS55340.
The ideal lossless boost duty cycle for Vin = 12V and Vout = 25V is D = 0.52. Even with an ideal 100% efficiency boost converter, the required input current would be Iin = Iout / (1-D) = 2.9A / (1-0.52) = 6.04A. This current must be allowed to flow through the integrated low-side switch of the TPS55340, whish is only rated for 5A.
I do not believe we have an integrated FET boost converter in WEBENCH which can handle your input/ouput requirements, but we do have very high efficiency external FET boost converters that can. I would recommend checking out the TPS43061 synchronous boost controller.
Kris