As per refund rules cancellation done after 48 hours before departure of train will attract 25 % penalty.
Is the time of departure determined from the scheduled departure time of the passenger's boarding station or from the the originating station?
Originating Station departure is considered.
Proof: The best I can do is prove that if it is otherwise it is clearly mentioned as in this document, where "scheduled departure of the train from the journey commencing station" is mentioned
A good question indeed, the answer is a bit illogical but you have to consider the situation in which these rules were made to understand the answer.
Imagine you are travelling by Himsagar Express, a train that runs from Jammu Tawi (in Jammu and Kashmir) to Kanyakumari (in Tamilnadu), the journey spans a total distance of 3791 Kilometres over approximately 70 hours, however your boarding point is Ernakulam (in Kerala) and you are travelling to Kanyakumari, the distance here is only about 300 kilometres, technically when the train starts from Jammutawi, you are technically more than 48 hours prior to your departure time, but the chart for the train has already been closed and booking is also closed already.
The ticket you just cancelled cannot be allotted to anyone else in the waiting list, so technically its a loss for Railways and hence you will be charged 50% cancellation fee (applicable from 4 hours prior to departure of the train).
The time of departure is determined from the scheduled departure time from the the originating station. Once the journey has commenced, any cancellation/upgradation stands invalid as the passenger list/chart will have already been prepared.