I too had the old style guide rod on my LC9s (purchased in August). Called Ruger and complained about reassembly problems and they sent me out the new style one in a few days.
When I first went to the range with the new guide rod, I had a lot of FTF issues. Took the gun home, left it locked open (slide back) for a few days, and tried it again. It now works perfectly.
In regards to the comment above about the guide rod on a new LCP, my latest LCP (purchased about December of 2013) showed that same "galling" evidence after one range trial. Called Ruger and was told that this was probably due to their doing away with the "bell shaped" inner spring that used to be installed forward in the gun. They suggested that I send the gun back and they would "open up" the hole in the slide where the guide rod feeds through.
Not wanting to do that, I purchased the upgrade stainless steel guide rod and 13 pound Wolff spring from Galloway. The LCP has worked perfectly since then. It even seemed to dampen the recoil slightly with the 13 pound spring.
I noticed that Galloway now lists a replacement guide rod and spring for the LC9s. However, my LC9s is working so good, I think I will just keep it stock.