In the CCleaner->Options->Advanced, there is a setting "Only delete files in Windows Temp folder older than 48 hours", that's probably the reason ccleaner doesn't delete everything sometimes, you should leave it enabled.
I never use the "Analyze" button anymore, I just press the "Run Cleaner" button.
Also I always save a backup .reg file if there are more than 5 issues, when I "Scan for Issues".
CCleaner works great, i've never had a problem with ccleaner, best cleaner i've ever used.