UPDATE: SOLVED
Hi pycage suggested to do a dskchk/file repair and this identified and solved the problems. If Conky or similar is showing Trackerd at high CPU annd your n900 is acting funny, I suggest you also try this resolution.

Original Post
Help:
I don't know how this has happened but my whole MyDocs folder has copied/replicated themselves inside a music folder that was already inside the original MyDocs !

Series of events:
1) I loaded 2 new mp3s to the phone last night via Windows Media Player sync
2) n900 did not pick these up in the media player
3) This morning I tired to connect via USB, said that device storage in use.
4) ran lsof | grep MyDocs and found trackerd was accessing a number of files
5) Killed it
6) Connected via usb successfully
7) Opened the folder (Music) and found all the MyDocs folders files replicated inside
8) tried to delete the duplicates, wont delete (in use presumably?)
9) Tried to delete manually from device, same thing.
10) Media player wont update new files and I cant delete the replicated MyDocs....

WTF is going on here??? I hope I dont need to reflash, help !

oh oh...this is getting worse. It seems there is an infinite folder structure showing...eg I open the music folder and see all the MyDocs folders, I go into this and open music again and see the Mydocs folders again etc etc...keeps going deeper and deeper in the folder levels. Now I have deleted my images folder and all levels show this gone now...?

did you create a symbolic link perhaps? if you deleted your files you may be in trouble. backup all your files now before you proceed any further you shouldn't need a reflash but backup all your important files so you do not delete them by accident..

cheers. I deleted (what I thought were replicated) files. Stupid. I have a back up file...but it wont restore to the current device as the 'settings' part throws an error. Is there a way of getting a clean MyDocs or is that simplifying it too much

In a terminal do

find . -type l | more

keep hitting enter looking for the file that is something like
./MyDocs/Music/MyDocs

or whatever the directory is like.

If you delete just that link everything should be ok.
I'm not sure what is happening with your backup restore though, need more info.

Hi Cue. Doing the above command gives me the following:

find: ./.gnupg: Permission Denied
find: ./.MyDocs/.documents: Input/output error
find: ./.MyDocs/.apt-archive-cache: Input/output error
find: ./.MyDocs/.espeakGU: Input/output error
find: ./.MyDocs/MyPaint: Input/output error

These look like the files I deleted thinking they were duplicates actually.

I ran the command in user

trackerd is running constantly at 80% or more...I assume cause of the file mix ups it is getting confused and hanging.

any ideas?

Maybe the file allocation table got corrupted (FAT filesystem doesn't support symlinks, so a symlink cannot be the reason to get into an endless loop under MyDocs). Have you tried repairing the filesystem when connected to a PC via USB?

worked pycage. Thanks so much. I will edit the original post to help others if needed.