This was way too long to post in on the sign board or even on Twitter. Using warps between the Nether and the Normal doesn’t work as intended. What happens is if you try to warp to a point in the Nether while still in the Normal world, you are transported to the same XYZ coordinates as where you left from in the Nether. You are NOT taken to the spot where the warp is. Example:
A warp called Derp (not an actual warp) is set in the Nether at -32,64,48. You are at 0,64,0 in the Normal world. When you try to warp to Derp, you are instead teleported to 0,64,0 in the Nether and not to where Derp is. Once IN the Nether though, warping to Derp will work as intended. This works the other way around, being in the Nether and trying to warp to a location in the Normal world. The same thing will happen. I’m not sure if this is a bug with the Bukkit server or with the Essentials plugin, or if it’s even fixable. I’ll put up more information as I find it.
UPDATE: It appears this is fixed with Bukkit build #860.