I have the same issue. All plugins, woocommerce, wordpress all up to date as of today. Bank Transfer, Paypal. and Paypal Payments Pro enabled. Tried removing and reinstalling the plugin. Tried activating and reactivating. Settings are visible in the database table but not visible in the checkout options. Save changes button is the only thing visible in the settings.This has occurred on 3 different live ecommerce sites i manage. One of those sites I was able to set the API settings etc before updating Woocommerce. After updating Woocommerce plugin the Paypal Pro settings disappeared? Plugin still works. Credit card transactions are still happening OK. Just no access to the settings.
On another site the Paypal Pro settings never appeared after the first installation of the plugin so am not able to set any API settings etc.
Sites: renewme.com.au facerobics.com.au dave.com.au. Two of these are still under construction.