I just completed MEPS last thursday. I have wrestled and played baseball my entire life, including college. Needless to say I'm a little banged up. And to make matters worse, I had a baseball game the night before where I dove to catch a ball and came up a little lame after jamming my knee in the ground. Nothing major, just a little swelling around the patella, however any side to side movement hurt a bit. The entire day at MEPS, I was getting up and sitting down in chairs (as opposed to standing in line). So I was in a bit of pain the whole time. However, the Ortho portion of it where you have to do all the physical movements was relatively quick. And I'm certain that if you've been a catcher all your life, then you know a little bit about 'sucking it up' and just ignoring the pain.
Walking on the knees, as well as doing the kicks, was a bit painful on a bad knee, but as long as you don't make a face or anything, you'll be fine. As long as you don't have a serious, debilitating injury then don't worry about hiding a little bit of pain and it's over quick. A little bit of pain for a few minutes is well worth it.
No worries, you'll be fine.