Yesterday I baked a bunch of cookies and as they came out of the oven I put the RBC on them. As they sat for a few minutes some of the RBC started to sweat-like. Not all of them did this though.

Why do you think this happened? I used a recipe with Crisco. My thought is that I could have waited for a minute or two before putting the RBC on the cookies because maybe they were just too hot just coming out of the oven.

I can tell too which ones were the ones that sweated as they don't look as smooth as the ones that didn't.

It would be my guess, that the cookies were a bit too hot, and the shortening melted a bit. You could try polishing the ones that aren't as smooth by rubbing it with your warm hand? But I'll bet no one else would notice a difference, unless you tell them.