New iTunes doesn't see all music in iTunes folder

I recently upgraded to iTunes 9.1.1.12. Since the upgrade, I notice that it only shows a portion of the files in the iTunes folder.
I can see them when I open the folder in Windows Explorer.
I haven't/don't receive an error message.
How can I correct this?

From Germany with not perfect English:
I had similar problem. Files that were not transferred had either no file-ending (.tif and .jpg-files without these endings are not synct) or a wrong ending (.pdf for example).
And the Apple-Hotline told me, a next iPod-software-update would allow a better sorting photos on the iPod. (Actually you can not use folders in folders, and all Photoes are sorted by date; a little help may be a count-number at the beginning of the file-name: 01.... 02.... 03... This helps, however it is not a good work for so many photos as you have.)

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    From Germany with not perfect English:
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