I don't think it's a problem with the supplementary estimates; it's a problem with the main estimates. The 44% that you mentioned is interesting, because it was the following year: this year. Last year, in the main estimates, you could see 70% of the spending measures included. The reason is simple; it was a big chunk of money under the infrastructure program. It was easier for the government and Treasury Board to include it in supplementary estimates (A) following the budget. It was not the case the following year, because the infrastructure program was not there anymore, and therefore all these smaller programs and all that were more difficult.
The problem is the beginning of the fiscal year following the budget, with the supplementary estimates (A), where you're supposed to have most of the expenditures that were not in the main estimates.