Good idea on flagging the required ones (however we'll make this much easier in v8 and be automating this and changing permissions via ftp using php when possible), but we will definitely mark the required ones.
On your specific issue, what is probably happening is the files within aren't writable. If you click on one of the folder names with a FAIL, it should expand and show what is failing.
The big ones that you need to pass are:
cache
gallery (if you are using gallery forums)
includes
sessions
styles
tmp
