[Marc Brown] “This is Blu-ray. Although the two are effectively interchangeable in Encore.”
That may be the view from the application user interface, but beneath the hood, the formats are of course quite different.
This doesn’t happen when authoring a DVD from Encore, so it would appear to be a limitation of Encore’s current Blu-ray implementation.
Your workaround is probably the preferred workflow, until this is addressed by Adobe. I’d recommend you call Tech Support or go to Adobe’s web site and enter a bug in their support section.