I had this issue with Crashplan simply keep analyzing files but not backing them up. I finally figured out the cause and resolved it.
One cause of this issue is from incompatible file permission. I am not sure exactly how some of my files end up with different permission than others, though I suspect it has to do with migration of files from old computer to new computer over time. I notice that Crashplan cannot backup files with permissions specified only for my user account, but Crashplan can backup files with permissions specified for my user account, SYSTEM, and Administrators.
You can see what permissions are defined for whom if you right click a file and select the Security Tab:
Under the "Groups or user names" section, you see SYSTEM, user (Network\user), and Administrators (Network\Administrators). Crashplan can backup the files with these three users having full permission. For the files that Crashplan simply keep analyzing without ever backing them up, only the user account permission is defined -- lacking permission for SYSTEM and Administrators.
To fix this, I go to the top level folder, which happens to have the correct permission. I click the "Advanced" bottom at the lower right hand corner. At the bottom of the Advanced Security Settings dialog box, you have the option to make everything (files and folders) inside the folder inherit the permission of the top level folder. (I.e., select "Replace all child object permission entries with inheritable permission entries from this object" and click ok.)
