Hi Wan,
I am sorry to hear that you were delayed due to the weather.
Unfortunately no refunds are given due to bad weather conditions as per the JR terms of usage:
Once use of the PASS has begun, no refund or extension of the validity period can be made in the event of train non-operation, delay, or the like. No refund will be made for transportation, accommodation, or other fees incurred as a result of schedule changes.
You can find the complete usage conditions here:
http://www.japanrailpass.net/eng/en008.html
Hope this answers your question,
Daniel