In fact, they usually are done for very solid, very good management reasons, in my experience at least. I can't speak specifically to each and every one of them included in the supplementaries.
They're done because conditions for the release of funds have not yet been met. It's to ensure that funding is released to departments only when the specific conditions have been met. For example, certain triggers have been met, the department is ready or it has fulfilled its obligations as stated in the Treasury Board submission, for example, or in a memorandum to cabinet. It is usually a good financial management practice to have frozen allotments to ensure the funding is released only when it's appropriate to do so.