Rather than using the nipple wrench to start the nipple in the hole, just use your fingers to get it started. I think you'll get a better 'feel' for when the threads locate. Also, like Mykeal suggested, take one of the other nipples out & try it in one of the stubborn holes, that way you'll know if there's problem with the thread in the cylinder.
"For a man, be he ever so much resolved to do his duty as a parent, can't be flogging his children all day....."
The Memoirs of Barry Lyndon, Esq. (William Thackeray).