OK, that was correct, these folders Applications in the HomeFolder and in the MacintoshHD folder are not the same, that also goes for the ApplicationSupport Folders.
Did you do the exclusion of the Application Folder from the beginning (I am interested why you did that at all) ?
If not, does the TM backup contain the ApplicationSupport Folder from an old date?
As I said I can not simulate your issue.
I checked the permissions in my mac with (see the post of dot.com):
ls -lae@ /Applications | head
and the result is the same as dot.com:
total 352
drwxrwxr-x+ 67 root admin 2.2K Jan 18 09:55 ./
0: group:everyone deny delete
drwxr-xr-x@ 38 root wheel 1.3K Jan 18 11:06 ../
com.apple.finder.copy.checkpoint#N 8B
com.apple.finder.copy.source.inode#N 8B
com.apple.finder.copy.source.volumeuuid#N 36B
user.nalp6b0 2.0K
-rw-rw-r-- 1 root admin 30K Jan 18 11:04 .DS_Store
-rw-r--r-- 1 root wheel 0B Jul 31 00:56 .localized
a basic, but important, difference is that you have two lines giving you mores permission to act on folders:
1: group:everyone allow list,add_file,search,add_subdirectory,delete_child,readattr,writeattr,readextat tr,writeextattr,readsecurity
and
1: group:everyone allow read,write,append,readattr,writeattr,readextattr,writeextattr,readsecurity
I don't know how or why you did that, but it may be important (as Barney thinks also).
Another point is that some non-Apple apps will not run correctly when the ˜/Library/ApplicationsSupport Folder is not there, but you don't notice because it is on your mac, but not in the TM backup.
If you did not do it yourself, this can be caused by a compromised or illegal third party app/tool/preference.
Lex