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Have you tried clearing the media store and letting it rebuild?
From the iSyncr FAQ.
I have problems with my playlists, what should I do?
Your phone has an internal cache where it stores this information. Sometimes this cache gets out of sync. You can delete this cache by looking for an application called "Media Store" (or similar) in "Settings->Applications->Manage Applications". You may have to press the menu button and change the filter to show all applications. Once you find "Media Store", open its options page and select "Clear Data". Then reboot the phone to force the cache to be rebuilt.
If that does not do it, there may actually be duplicate files on the phone. If so, try
What about removing music, will iSyncr remove playlists when I want new ones but am out of space?
Yes... if you select "Remove Music Not In These Playlists"