I assume because you specify the browser in you post you mean Ghostery add-on for firefox.
You need to figure what files are being removed and exclude them from cleaning
The easiest why do achieve this is to uncheck everything on both tabs of ccleaner, and then follow this method
Place a checkmark in the first item (if this is the add-on for FF then I would jump down the list and try the Firefox entries first).
Run a Clean, DON'T CLOSE CCLEANER
Open your browser, is ghostery broken
If yes: look at the logs of what was cleaned one of those items is likely the culpert add it to your exclude list. If no: uncheck the item and check the next item
repeat steps 2-5 until you find the item being removed that causes the issue, if non of the browser entries cause the issue, move on to all other entries in using steps 2-5
I have Firefox 11 and the Ghostery extension, and CCleaner doesn't touch it's settings for me, although that doesn't say it isn't touching yours for some reason.
My install of Ghostery maintains it's settings in the following file ...
"C:\Documents and Settings\<username>\Application Data\Mozilla\Firefox\Profiles\4hxrc27e.default\Extensions\firefox@ghostery.com\defaults\preferences\defaults.js"
I'm on XP by the way, and I made sure it was the correct location by temporarily disabling it.
Can you check if yours is saved in the same location, which is a good place for us to start, and then post back.
EDIT: It was my turn to do the Ninja thing Nergal.
I think I have found out the reason for my problem.
My browser is Firefox....but I run it Sandboxed (Sandboxie)!...
I had installed Ghostery in the sandboxed mode!
I switched Sandboxie off and looked at the Firefox extentions. Ghostery, although it was appearing in the sandboxed mode, it was NOT there in the non-sandboxed mode...
I downloaded Ghostery in the non-sandboxed Firefox and run CCleaner.
I am delighted to say that CCleaner does not delete Ghostery any more.
It is said that Sandboxie has a very steep learning curve. They are not exagerating....
I have been using Sandboxie for over a year now, but there are still occasions when I am caught out.
Thanks for posting back Basil, and yes, Sandboxie can catch you out at times and setting it up exactly as you want can take some time.
One I remember is my daughter trying to print off some invoice for something, and she couldn't get the printer working. This was my early Sandboxie days, and it took a while to realise that it wouldn't work because she was sandboxed.
And relating to your comments above, I always launch Firefox un-sandboxed to install new extensions. Or take advantage of the sandbox to try out an extension before deciding to keep it or not.
Same for me and Powershadow + Sandboxie. When all else fails, changes are gone after a restart.
On more serious matters, Hazel, I shall defend to the death your honor and your right to Sandbox or not as you choose. Those n'er-do-wells who do not are to be chastized and roundly condemned. DON'T MAKE ME come over there!