Whenever you have any strange mesh behaviour, start by:
(Do these, even if you are sure you don't need to.)
You sometimes get a cleaner UV unwrap for a hard-edged object by using conformal unwrapping instead of angle-based. But conformal unwrapping is more sensitive than angle-based to the exact location of the seams, and can go horribly wrong if they are not well placed.
When baking texture from a high-poly object to a low-poly one: