Older versions of AtomicParsley seem pretty broken. Don't use them. Not to mention the newest versions containing such non-sense as:
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--metaEnema , -P Douches away every atom under "moov.udta.meta.ilst"
--foobar2000Enema , -2 Eliminates foobar2000's non-compliant so-out-o-spec tagging scheme
Need I go on? This all seems very "immature" to me, and biased against foobar2000's adoption of Nero tagging scheme.
Anyway, when using the latest AP (0.8.8) version on files encoded by iTunes or Nero that are untouched by previous versions of this software, I'm not able to reproduce these problems. I would however suggest you stay away from this software as testing shows it is pretty touchy and full of hacks.
You can use foobar2000 to set tags using the command-line as well:
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Usage:
/tag:help - displays this message
/tag:<command1>[;<command2>;<command3>...] <file1> [<file2> <file3>...]
Commands:
<NAME>=<VALUE>
Sets <NAME> field to <VALUE>, e.g. "/tag:title=test <file>".
You can erase particular field by specifying empty value, e.g. "/tag:comment= <file>".
You can also specify multiple values by separating them with \ character, e.g. "/tag:artist=name1\name2 <file>".
AUTOTRACKNUMBER
Sets TRACKNUMBER field of multiple files according to their order in commandline.
E.g. "/tag:AUTOTRACKNUMBER <file1> <file2> <file3>" will assign TRACKNUMBER=1 to <file1>, 2 to <file2> and 3 to <file3>.
FORMAT:<FIELD>:<SPEC>
Formats <FIELD> using <SPEC>; see title formatting manual for more info how to use it.
E.g. "/tag:FORMAT:COMMENT:"%ARTIST% - %TITLE%" <file>".
GUESS:<PATTERN>:<SPEC>
Guesses field values using <PATTERN>, according to <SPEC>.
To perform "guess values from filename" action, use "/tag:GUESS:<PATTERN>:%_FILENAME% <file>".
E.g. "/tag:GUESS:"%TRACKNUMBER%. %TITLE%":%_FILENAME% <file>".
Hope this helps.