Interesting, didn't realize the patcher did that bugfix.
What is probably going on is that the directory you installed your client in has some kind of write protection that the patcher isn't able to work around. What OS are you using? While there's probably a setting you can tweak to avoid the problem, if you just move the whole client to a new directory (I would recommend creating a C:\Shards of Dalaya\Client) then the patcher will most likely be able to work as intended.
Alternatively, you can open your client directory (i.e., the place you installed Everquest) and rename that file (lavastorm.eqg) yourself (you'll probably also have to rename nektolus.eqg as well -- it suffers from a similar bug).