It could be indexing the files. Suposed to make file searches faster, never seen much increase myself.
If you use ext3 or reiser file systems then it may be updating the journals. It does that so that if you crash you don't loose anything.
Go to a term and type in top and watch to see what is running. index thing is usually updatedb but sometimes is done inside GUI if you use KDE.
Someone else may have more ideas.
Later
edit: Can't type worth crap