Anyone having issues with large packages not updating on BDP's, here is probably the answer:
KB973762 - A package that is several gigabytes in size is not updated on a branch distribution point (BDP) in System Center Configuration Manager 2007 Service Pack 1
Read the complete post at http://wmug.co.uk/blogs/r0b/archive/2009/12/02/new-configmgr-kb-article-kb973762-a-package-that-is-several-gigabytes-is-not-updated-on-a-branch-distribution-point-bdp-in-system-center-configuration-manager-2007-service-pack-1.aspx