This is only an apparent contradiction. The planned spending in the main estimates and the RPP is really just that—a plan. The DPR recognizes the actual spending done and registered at the end of the year. The $44 million reflects an acceleration of work, mainly on the West Block and the Sir John A. Macdonald Building. So it is still within the approved budget.
On March 24th, 2015. See this statement in context.