I am running the recommended build, and whenever I run it and get on everyone looks like steve. Some people get overflows and are forced to leave. I had to reset the world to fix a bug where I couldn't break or place blocks. I only have 4 plugins. Factions, Orebfuscator, nocheatplus and craftbukkituptodate.
Skins are controlled by Mojang, not the server. Moved to the correct forum. Try removing your plugins and seeing if your other issues are still a problem.