ITunes issues - corruption, confusion, replication,

Question

Hi,
I'm sure this is really simple and over time i have completed complicated the issue and i just need some clarity.... here goes....
SET UP
Synology Nas with a share on it called iTunes (for the purpose of this lets call it the U:\)
Desktop pc running windows 7 ultimate
mac book pro retina with osx
Apple TV
iPad mini
iPad 2
iPhone 5s
iPod nano (6th Gen)
History:
A while ago I decided to move my iTunes library onto my nas drive to be able to access it from my laptop and apple tv etc. Somehow the library file or database corrupted and wiped half of my playlists, songs etc. I ended up manually sorting everything out (TWICE!!). this also wiped my iphone backup and subsequently my iphone when i plugged it in next.
After purchasing my mac book a few weeks ago I was hesitant to mess around with a working library but today I took the plunge. and wish I hadn't. Sudenly all my playlists could not find the associated tracks either on my pc or macbook. Fortunately i have a backup library file so i copied and renamed it and all seems ok. until i try to point to that file on my macbook at which point it starts updating the library and off we go again.
How I add files to iTunes
Now i know this isnt the right way to go about using iTunes but its how i first started using it years ago (iphone 3 days) and since then its grown and grown and i havent been able to sort it out. so this is how i add music to my library and playlists:
U:\Manual copy\iTunes library folder - DO NOT DELETE OR MOVE!! - I place the mp3 in this folder
Then in iTunes File > Add file (select the file, sorted by date order so its the first one in the list, and add)
In songs, select the file, right click and add to the playlists i want it in.
This essentially means i have two copies of the file right? assuming iTunes creates a backup or a copy somewhere?
iTunes Settings:
My Current settings:
The library file is located in: U:\iTunes Media Folder:
My Current File Structure (on the iTunes share)
This just looks like a mess now and i have no idea whats what any more. ive expanded the folders i think are relevent.
So what am i after?
ideally i want to wipe the whole **** lot and start fresh. But my folder sizes are so huge im wary of loosing so much music, and having to rebuild 170 odd playlists - I setup albums as individual playlists and have different playlists for moods, genre, etc. Folder sizes:
U:\iTunes Media Folder\music - 81.2GB, 11,886 files
U:\iTunes Media Folder\manual copy\iTunes library folder - DO NOT DELETE OR MOVE!! - 32.5GB, 4503 files
i can see from Songs in iTunes that i have 11,596 songs added to the library. sorting by name shows that i have at least 3 copies of each song somehow!? ium guessing that happend when the original corruption occured and was a result of me panicking and trying to fix it.
So what is the easiest way to fix this? i really do not want to spend hour upon hour of starting a whole new library and adding each song one by one, or having to rebuild playlists (which are on all my mobile devices except the iPad mini). 
im also extremely weary of loosing my iphone backups and connecting my phone to itunes again incase i loose everything.
Can anyone give me some clear advice on how i should go about fixing this please? i tried looking through the community but i just got more confused.
if you need any further info / screenshots please ask.
Many thanks.
Hiten

Answer 1

Thanks for the reply, i double checked and everything on both pc and mac is set right:
both are opening the same .itl file
both have the media folder set to <NAS>/iTunes/iTunes Media
both have the two check boxes ticked (keep folder organised and copy) <------ could this be the problem?
So this is exactly what happens step by step, after having just restored from a backup:
PC
First I open iTunes on the pc, play some tracks - all fine.
Exit iTunes
Wait a minute or two whilst anything saves etc (just incase)
MAC
open Itunes on the mac (its already pointing to the right library)
it says "updating library" - really quick - maybe 10 seconds
all the songs look fine, until i try to play one.
the song could not be found, would you like to locate it? - click no.
Exit iTunes
wait a minute
PC Again
open iTunes on the pc again
"updating iTunes library" - takes a while - a lot longer than it took on the mac - approx 4-5 minutes
now all of the tracks have a "!" next to them
exit iTunes
wait a minute
Mac Again
open iTunes on the mac again
"updating iTunes library" - really quick again
now all the songs have the "!" next to them too.
exit iTunes
restore from backup again
Not really sure why its doing that to be honest.
Any ideas?
Regards,
Hiten