Downloaded this tool https://developer.valvesoftware.com/wiki/SteamCMD to test a different bug, it has managed to adjust all my regular Steam client settings to now point to the steamcmd install location. While its not directly a steam client bug, they could keep separate installs.

john@joran ~/.steam > ll
lrwxrwxrwx 1 john   23 2013-01-17 20:24 bin -> ~/.steam/bin32
lrwxrwxrwx 1 john   37 2013-01-17 20:24 bin32 -> ~/steamcmd/ubuntu12_32
lrwxrwxrwx 1 john   37 2013-01-17 20:24 bin64 -> ~/steamcmd/ubuntu12_64
-rw-rw-r-- 1 john 7225 2013-01-17 20:23 registry.vdf
lrwxrwxrwx 1 john   25 2013-01-17 20:24 root -> ~/steamcmd
-rw-rw-r-- 1 john    0 2013-01-17 20:24 starting
lrwxrwxrwx 1 john   25 2013-01-17 20:24 steam -> ~/steamcmd
-rw-rw-r-- 1 john    6 2013-01-17 20:24 steam.pid
prw------- 1 john    0 2013-01-17 20:22 steam.pipe