Unchecking selections in library doesn't "stick"

My library has exceed the capacity of my iPod so I went through my library in iTunes and unchecked a number of songs. Upon exiting iTunes, I did see the "saving library" progress bar, but when I opened iTunes again, some of the unchecked songs were checked again. Any suggestions?
Thanks!
Ned
Sony Vaio Windows XP
Sony Vaio Windows XP

An alternative to unchecking songs is to choose the update option "Sync Music - Selected playlists". If you do this you can update any of the existing playlists you have leaving some out or create a playlist specifically for your iPod and drag the tracks you want into it. If you tire of the list and want to change it, you just add or remove the songs you don't want the ones you take out out remain in the library to be used again. You can read more about playlists at these links:
iTunes: Creating playlists of your favorite songs
How to create a Smart Playlist with iTunes
Loading songs onto iPod automatically - Windows
Another option is to set the iPod to "Manually manage songs and videos" and drag whatever you like to it: Managing content manually on iPod
Unchecking boxes can have other effects that may outweigh any benefits to be gained from using them to manage an iPod. The check boxes have a few uses:
Unchecked songs will be skipped when playing songs from the library or a selection. They will only play when individually clicked on.
Smart Playlists have an option that unchecked songs won't appear.
Unchecked songs will not be burned to CD.
iTunes: Understanding the Symbols Next to Songs

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On rare occasions, MediaSource 3.30.2 will produce an ID3 tag that MP3-Library doesn't like. (This is pretty rare -- out of 45 tracks I updated the tags on, 6 did this.) This results in the file being displayed as corrupted. If you select "Analyze/Fix MP3," it finds a frame or two with random specifications at the very start of the file, followed by a single bad frame, and then all good frames.
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File size: 3,63,232 bytes
Offset to first frame header: 2,630 bytes
MPEG version .0; Layer III
Bitrate: VBR (Xing); Sample rate: 44,00 Hz
Channel mode: Joint stereo
Private: No; CRCs: No; Copyrighted: No
Original: No; Emphasis: None
Frame size: ,52 samples/frame
Frame length: 47 bytes/frame (unpadded)
Pad size: byte(s)
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Estimated time: 3:54 (234 secs.)
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File size: 3,63,232 bytes
Offset to first frame header: 2,630 bytes
MPEG version .0; Layer III
Bitrate: VBR (Xing); Sample rate: 44,00 Hz
Channel mode: Joint stereo
Private: No; CRCs: No; Copyrighted: No
Original: No; Emphasis: None
Frame size: ,52 samples/frame
Frame length: 47 bytes/frame (unpadded)
Pad size: byte(s)
Estimated frames: 8,945
Estimated time: 3:54 (234 secs.)
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Offset to first frame header: 2,600 bytes
MPEG version .0; Layer III
Bitrate: 224 kbps; Sample rate: 44,00 Hz
Channel mode: Joint stereo
Private: No; CRCs: No; Copyrighted: No
Original: No; Emphasis: None
Frame size: ,52 samples/frame
Frame length: 73 bytes/frame (unpadded)
Pad size: byte(s)
Estimated frames: 4,96
Estimated time: 2:0 (30 secs.)
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Unchecking selections in library doesn't "stick"

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