Binary/ASCII File upload issues

[nocturnal]

if i do file index.php on a file i uploaded that works just
fine with php ran as cgi i get "/path/index.php: a
/usr/local/bin/php script text executable" and if i do file
index.php on a customers index.php file which i think they
uploaded using binary transfer mode i get "script text
executable/bin/php" only, the second file doesn't work using
php as cgi, i get an internal server error, i know how to
fix this but i'm wondering if anyone could explain why this
happens on freebsd and if it's related to the ftp transfer
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