The load on your shoulders is both much different and potentially much much higher. You should probably take a look at technique and grip width. Also make sure your shoulders are specifically strong for this type of pushing. Your body might just not like (flat) benching. Some people's don't. Not much to do then, but just accept and move on. If you don't have some specific attachment to or need for the movement, you don't really need it.
Maybe try real pause benching with lower loads exclusively for a while. Doing them exclusively on lighter days or on your warm-up sets gets plenty of reps in at some point down the line. Great to get the bracing and technique right and to get your shoulders strong enough in every phase of the lift.
And honestly, just be careful. If you feel pain in a movement, don't do it. You only get one set of shoulders, don't fuck them up for something ultimately unimportant. Having a functioning shoulder every day is much more important than a PR if you're not competing.