I was having the same problem and emailed Zennaware's Cornerstone support. They sent me these instructions that seem to have fixed the problem for me:
Quit Cornerstone
Open Terminal
Copy paste the following line into Terminal:
defaults delete com.zennaware.Cornerstone HistoryCacheUsage
Press return
Open Finder
Select Go->Go To Folder…
Enter:
~/Library/Caches/Cornerstone
and click “Go”
8. Move the selected directory (“Cornerstone”) to the Trash.
9. Restart Cornerstone
The next time Cornerstone prompts you to cache the repository log, choose “Never”.
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