The amount paid to the players are based on their availability for the matches. If a player was available for all the IPL matches, then that player is eligible for the full amount. If the players were not available for some matches, then they are paid on a pro-rata basis.
In the above case, Ponting and Maxwell were available for the entire season. Missing a match due to injury or benching is not considered as unavailability and hence they should be getting the full amount. There was a rule that if a player was available for a certain no of matches and misses only a certain no of games, they should be paid the full amount. Not sure if this rule is still there.
Also note that the amount offered to the players vary based on certain other criteria as well. For eg:- if the team didn't qualify for CL, players will get only 80% of the auction rate. Players also might get some % of amount if their team wins the IPL or finishes at 2/3/4. However there is no clarity on this and it depends on the team. Players also have to pay the income tax in India for the money they earned.
Source: News, read somewhere