I was able to reproduce this with the same configuration: Google Chrome 15.0.874.106 m (latest final version, no beta); CCleaner V3.12.1572.
Here's the steps I took to reproduce the problem:
1. Set CCleaner's Chrome Settings (check the boxs) as follows: Internet Cache, Internet History, Cookies, Download History, Session, Saved Form Information.
2. Start Chrome.
3. Clean a session with Chrome's native cleaner (Tool icon, Tools, Clear Browsing Data: Clear browsing history, Clear download history, Empty the cache, Clear saved Autofill form data). We leave Cookies unchecked so that CCleaner can manage them.
4. Close Chrome.
5. Start Chrome; access any 10 urls.
6. Close Chrome.
7. Run CCleaner with the clean settings listed in step 1 above.
8. Start chrome.
9. Access new tab. Most Visited URLs show only the two default URLs. It appears Chrome is clean.
10. Access a second new tab. Two default URLs are listed as are the 10 recently visited sites from step 5. Using Chrome's native cleaner, this same process would have wiped the non-default URLs regardless of how many new tabs were opened.
Note: Assumes no changes have been made to default New Tab page and that the Most Visited selection at the bottom of the page is selected.
End of test.
In this test process, all URLs are from shortcuts. None are typed URLs. Chrome browser user does not have Administrative rights but has Power Users rights.
Chrome's native cleaner (step 3 above), makes changes to two files that CCleaner does not. Both files are in:
C:\Documents and Settings\USERNAME\Local Settings\Application Data\Google\Chrome\User Data\Default\
It is likely changes to these files are why Chrome can clean the old URLs and CCleaner does not but I'm not technically savvy enough to get into these files to determine why.
CCleaner version 3.13.1600; Chrome version 15.0.874.121
Problem still exists in Step 10 of test.