It is interesting as time goes on, what things are found by others that have already been reported, but seem to be ignored. SQL 2005 Clustering issue with lower case servernames is the topic of this post.
I attended a Clustering Class by Russ Kaufmann and during the class I illustrated to him a problem that we had in installing a Windows 2003 Cluster with SQL 2005. This issue was if you had your physical server name in lowercase, when you installed SQL 2005, it would fail and rollback (partially at that time) the entire install. I went round and round with a Connect Item and could not get Microsoft to repro this, even though I had reproduced this on demand many, many times.
Now I find this post from Tara Kizer on SQLTeam.com blogs. This post illustrates that when physical servernames are in lowercase there is an issue with the install. I also found the reference to this post by Microsoft PSS illustrating the problem as well.
Now the only difference is that my issue was reported in 2007 and these posts are from 2009. Also my Operating System was Windows 2003 R2 and this is referencing Windows 2008 Server. It is still amazing that this is not fixed in Windows 2008, but I just had to get this off my chest.