This thread is resolved. Here is a description of the problem and solution.
Website has been using EUC-JP as an internal character encoding for mbstrings (mbstring.internal_encoding option). In this configuration PHP generates reported notice for every script that is using filter_input functions to filter strings (not only for WPML).
We've fixed this by changing internal encoding for mbstrings, by setting mbstring.internal_encoding to UTF-8 in htaccess file (using php_value directive).
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