I assume you are referring to the military press. These are very hard on the rotator cuffs, which is probably making the clicking/grinding sound. I like these exercises myself, but am very careful b/c they are one of the riskiest exercises out there as far as causing an injury.
It is very important to not overload the weights here - it is NOT the exercise to try to show off on! My father, who was very strong at these, screwed up his rotator cuff doing them and had to have surgery at a young age (twenty-something). Not only can he not perform these exercises at all anymore, it has affected his ability to bench press as much, etc.
I learned from his mistake, so I hope you can take this one a step further and learn from my advice.
Edit: One other thing. If you are actually hearing noises/feeling any discomfort, give it a break for a while and resume with the aforementioned caution.
It is very important to not overload the weights here - it is NOT the exercise to try to show off on! My father, who was very strong at these, screwed up his rotator cuff doing them and had to have surgery at a young age (twenty-something). Not only can he not perform these exercises at all anymore, it has affected his ability to bench press as much, etc.
I learned from his mistake, so I hope you can take this one a step further and learn from my advice.
Edit: One other thing. If you are actually hearing noises/feeling any discomfort, give it a break for a while and resume with the aforementioned caution.