Hi Patrick,
I already discussed this on the MS partner support forum with Stephen Ding (http://social.microsoft.com/Forums/en-US/partnerdevvs/thread/9d71d51e-d45f-4fdf-a138-d87902dd6c57). I sent him a simple test template and he verified that the managed .NET signing code is good, so in that respect I doubt that there's some method call ...