What is most likely happening is the bolt is dropping in that position, if you are pulling too far past half-cock to turn the cylinder and drop onto the pins. If your bolt is dropping before the half cock, or too close to allow loading, etc., you will need to retime the bolt.
That being said, it is not good practice to draw a hammer to half-cock and then fully lower it from that position, as the bolt can lock up without resetting and everything is locked, as the bolt is in place and the hand cannot rotate the cylinder, requiring removal of the barrel (or cylinder in a SAA) to free it up again. From half-cock the hammer should be drawn to full-cock every time before lowering it. This is true for any Colt type single action.
It is not good practice, either, to trust the "safety" pins, if you look at any older well used repro, and certainly, an original Colt, you will see those pins are usually battered out of existance. The R&D 5-shot drop-in cylnder for the 1860 has 10 locking notches, so the bolt itself is holding the cylinder safely between chambers, which allowed SASS to approve the 5-shot configuration.
Regarding Little Bear's comments, yes, caps can be mashed so flat that they are laid up on the frame, almost invisible, in front of the hammer, keeping it from fully dropping, and can only be removed with a sharp knife blade to peel it off the frame. Down inside, cap fragments get between the sear and hammer, etc. and lock things up.
Cap fragments in the action are most likely caused by excessive blowback through the nipple vent, solved a couple of ways. Replace the nipples (especially Ubertis) with Treso or Thunder Ridge Stainless nipples, which are a perfect fit for Remington #10 caps, the only size/brand you should use. The nipples have a smaller diameter vent hole, allowing less blowback, yet a hotter flame, and the correctly fitting caps are less likely to blow off and back into the action.
