I first ran into this issue with a mod that I was creating, but I have since confirmed that the issue also affects the wayshrines in the Falmer Valley that are part of the Auriel's Bow quest. I have confirmed this with no mods active other than Dawnguard and the hi-resolution texture patches.

It appears that on many occasions, when teleporting from one wayshrine to another that the player is exiting on the landscape below the wayshrine and not on the floor of the wayshrine itself. This is also apparent when the game is quit immediately after exiting a portal and the autosave reloaded. This issue manifests itself as the player slowly rising to the floor level upon exiting a portal, or when the autosave is reloaded (seems to be much more frequent with the autosave). Fortunately, the landscape under the Falmer Valley wayshrines is flat and the issue is not that pronounced:- this certainly wasn't the case when I modded wayshrines into Tamriel where the landscape was sloped (and I had to fill in with rocks on the lower side).

Would greatly appreciate someone at Bethesda taking a look as this particular mod of mine is on hold pending a resolution. This seems to be a bug that was introduced in Skyrim 1.8 - I had no such issues with 1.7.