If I run Analyze after running Run cleaner 2 files remain
Unless you have set any exceptions then these will probably be temporary files used by your Operating System.
(Logfiles, temporary files, etc.)
They could also be files used by some other programme you have running in the background.
As soon as you clean/delete them the Operating System (or background app) immediately recreates them, usually as an empty file but it may put a bit of data in there straight away.
So if you analyze again you see them again, the computer recreates them more quickly than you can click the Ananlyze button.
Try taking a look at the size of these particular files before and after cleaning.
If it's been a while since you last cleaned you should see that they reduce in size when cleaned.
(They have been deleted and recreated anew).
any chance you can tell us the names of these two files?