Your H.264 assets are definitely a Blu-ray legal form, are they,
Tim, to check this, look at the transcode status column for bluray in the project bin. It should show "do not transcode."
I have checked some old Encore projects of mine, and where the assets were imported in a BR legal format, they show as the same size on both tabs.
That is valuable info, and suggests that there is a problem with the legality of the asset. But Encore does some odd things with bluray assets, so who knows.