Adding here that warps won't always face the right direction when put not only on glass, but on transparent blocks I've tested, glowstone, and slabs. Replacing it with a fully solid block like you did should correct the orientation though.

 

Old post can be found here. Same issue with half slabs as well

 

This is not a bug in the warping system but rather in Bukkit. On world change it takes a while to set the correct location which causes the glitch. You also don't need to do anything to "fix" your location, just wait a second and Bukkit will automatically place you correctly above the ground. If this is not the case however, and you somehow get into a situation where you cannot move freely after 1-2 seconds without jumping please tag me and andrew with the instructions to replicate that bug.

 

Were you in god mode? This only affects players who are not in god mode since it only triggers in cases where essentials thinks it needs to adjust your location somehow (maybe the actual warp location is in the air or something). If you're in god mode then it won't change your location.