After deleting the bulk rail unloader and then pressing ctrl-z it would paste it vertical in all cases. Copying and pasting works fine, also pasting and rotating a blueprint, the problem is only with ctrl-z

This is possible to fix, but difficult, because the Factorio API does not expose any events for when a player performs an undo.

a new problem with the blueprints is when you copy with a blueprint and paste it again, it does not count for the extra rails you add to it. so when pasting, one of the rail loaders will be one tile off.

Include at least one connected rail when creating the blueprint. I usually blueprint an entire station together.