As mentioned in the documentation of Iotawatt, ports 13 and 14 are dual use and each can be used as either an input for a current transformer or as an input for a voltage reference.
while using these ports as voltage reference, there is no problem. But, when i configure these ports as CTs (for measuring current), The microcontroller starts continuously resetting, and the functionality of the device is disrupted.
I would venture to say that probably 99% of the users of 13 and 14 are using as CT inputs. Direct reference three phase is very rare.
Above you state that when using as voltage inputs there is no problem. So configure as such and dump the message log. Alternatively you can remove the SDcard and copy out /iotawatt/iotamsgs.txt. Either way, you have provided no useful information and the message log should contain some clues as to the nature of the problem.