As adverbs with an adjective such as "surprised" that can apply to a greater or lesser degree, both mean "to a moderately high extent". One slight distinction is that "rather" tends to be used a bit more formally than "pretty". So if I say idiomatically they mean pretty much the same, "rather" would have sounded awkward there.

Not sure, but second sentence sounds much stronger, with emphasis on surprise.

"Pretty" is only used in American, not UK English. "Rather" can imply the surprise was unpleasant. For a pleasant surprise, it's better to use "quite." An option that works for any type of surprise, in any English speaking country, and can also be used with any type of adjectives, would be "really."