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With 23 September's nightly build, I managed to make Git staging view eat up 100% CPU cycles. Here's what happened (ensure Git staging is open): 1) Create a resource in the directory where your local repo is stored. (I created a patch which got saved in C:\Documents and Settings\Administrator\git\eclipse.jdt.core). 2) The resource is shown in the unstaged changes in the git staging view. I saw this is a distraction, and not knowing how to remove it from inside of Eclipse, manually deleted the resource from the file system. 3) Git staging view removed the resource, but started an indexing job which hogged CPU cycles.
I have no problem with that in EGit 1.3.0.201202151440-r. Can you try it again with the newest EGit stable version?
Using 4.1 I don't see the issue - probably we've fixed it somewhere between 1.1 and 4.0 :-)