ID3v2 specifies that tags are in latin1 format (whether this is always true is another story). Often filenames are encoded in UTF-8 on an ubuntu linux system. GTKPOD currently allows you to specify a character set when importing (either system default or a specific character set). However, ideally it would allow you to specify two character sets, or at least have a tick box to say whether the choice also applies to ID3 tags. This would allow the correct behavior when importing directories with some missing latin1-encoded ID3 tags (which would then tag using the file path encoded in UTF8).
This behavior was noted using:
libgpod/gtkpod version 0.99.13SVN
Linux ubitsu 2.6.22-14-generic #1 SMP Tue Feb 12 07:42:25 UTC 2008 i686 GNU/Linux
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forgot to include an address, please send any questions/comments to peter at laneta dot apc dot org.