Something's bothering me about this problem.
You say the problem has only come up when the nipples have caps on them?
A couple of things can cause that to happen.
If the nipples are rifle nipples they will be a lot longer than the nipples made for pistols.
From the shoulder on the nipple that tightens against the sealing surface on the back of the cylinder to the top end of the cone you put the cap on should measure about .270". That's about 1/64" larger than 1/4 inch.
If a rifle nipple has been installed, it will measure about .445" which is a shade greater than 7/16".
With this large of difference between pistol nipples and rifle nipples, it's easy to see why a rifle nipple in a pistol cylinder will stick out of the back of the cylinder far enough to rub against the guns recoil shield. Especially if a cap has been placed on the nipple.
Try to measure the length of one of the nipples in your pistol and let us know what you find.
Another thing that can cause a capped nipple to hang up on the recoil shield of the pistol happens to brass framed revolvers.
If the gun has a brass frame and heavy loads have been fired in it, several people have reported that the ratchet star on the rear of the cylinder has embedded itself in the brass frame.
If your pistol frame is brass, remove the cylinder and look at the frame right next to the place where the cylinder rotating hand exists.
If you see the impression of the cylinders ratchet in the brass material and if the impression is very deep, that is allowing the cylinder to move aft far enough to cause the caps on the nipples to hang up on the recoil shield (usually in the slot that the hammer falls thru.) even when the correct pistol length nipples are used.
If this is the cause, I'm sorry to say it isn't easy to make a long term fix to the problem.
A short term fix would be to fill the ratchet impressions with some sort of strong epoxy but because the cylinder recoils against this area each time the gun is fired, it won't take long for the cylinder ratchet to pound the epoxy out of the recesses.