Try going to saved variable folder and deleting the following files.
CharacterProfiler.lua
CharacterProfiler.lua.bak
GuildProfiler.lua
GuildProfiler.lua.bak
Then launch WOW make sure at the character select screen BOTH Guild Profiler and CharacterProfiler are checked and Load out of date addons is checked. Then manually rescan the Character AND the the Guild Roster (Clicking save in Guild pane and in Character Pane).
Then click LOGOUT not exit. GO back to character screen click back then click quit.
Then upload CharacterProfiler.lua file only with password in the Guildprofiler text entry box.
If that doesn't work. Redo the same steps except when you come to the addons sceen at character selection TURN OFF ALL ADDONS except the 2 CharacterProfiler and GuildProfiler.
That will test to see if any 3 party addons are interferring with the actual addons during scanning.
Hope that helps
EDIT: Also make sure you ahve the updated patch for Roster to fix the parsing error due to Patch 2.0.3 Save Variables Change
Found Here:
http://wowroster.net/Forums/viewtopic/t=2289.html