4.4 GB Missing storage in ipod touch (really)

Question

Am am aware that my ipod touch came with 28 GB (not 32 GB) of free storage available.  This is a real issue of 4.4 GB having been lost.
ipod touch 4G  IOS 5.0.1  32GB
Settings>Usage>Storage says that I have used 12.1 GB.
Adding all the numbers for music and apps:
Music               6.9 GB
Medscape   61.7 MB
Skype      42.4
MotionX    37.1
IMDB       25.0
Yelp       22.7
Words      21.6
Sunrise    21.0
Weather    10.7
NPR         9.7
iheart      7.8
key ring    6.8
urbanspoon  5.4
wine ratings3.1
vegout      1.6
bad elf     1.1
gps info     .248
So 277 MB of apps plus 6.9 GB of music = 7.7 GB used.
12.1 GB - 7.7 GB = 4.4 GB missing
This probably happened while attempting to transfer music to the ipod from a Windows XP PC.  The transfer failed once partway through.  It worked the  last time.  The PC reports that the music library contains 6.9 GB.  All the music that I see on the ipod is the music that is in the PC library and there are not duplicates or other evidence of large spurious files.
What I would like is an app or PC based program that can look at the ipod file system, find the lost sectors and put them back into the available storage pool.
I really don't want reset the ipod back to factory settings and start all over again.

Answer 1

Thanks for your reply.  At the moment I don't think I need to check what you said, although I understand what you said about app size..
I used a third party tool to check the contents of the music folder (iPod/Media/iTunes_Control/Music/F47) in the ipod touch.  There were about 1775 mp3 files totalling about 10.2 GB. That is 3.3 GB different from the actual size of the music library (6.9 GB).  Thats most of the discrepancy.  This seems to confirm my suspicions that files got added to the ipod music folder without the library database being properly updated.  There must be some tool that can look at the files in the music folder and see if there are corresponding entries in the database and delete the files if they aren't in the database.
(The iPod is a gift and I am trying to remain optomistic about it).