I had to reinstall the OS in my 9550 as I was talking to RIM about a WiFi issue. Prior I backed up my hand held with DTM 6 and BBSAK 1.7
I tried to restore apps with BBSAK (I located all my .cod files at C:\Program Files\BBSAK\Backup) and after a very brief wait BBSAK said all applications were restored. However they were not restored to my phone.
I then clicked "Modiy COD's" tab, and install COD's and manually selected all the COD files.
Did you select the backup file when you did modify, load cods? Sometimes they don't all show up until I do a battery pull after the phone comes back up.