When you change Permissions from the Security tab of a Properties sheet, and then OK out, Explorer will erroneously turn off the archive bit. This will cause the file or directory to be skipped during an incremental backup.
The bug is a result of the way that Explorer orders its' actions on a Properties sheet. Changes made to permissions are applied immediately. When you OK, the General tab "sees" no reason to have the archive bit on so it turns it off. When the Permissions tab exits, it does nothing because it "knows" it has done its' work.
A workaround is to not click OK from the Security tab but switch to the General tab before you OK.