The value of customer fields of type version not converted to a version id while processing a received e-mail. It must be done like the issue field fixed_version_id.

The code in mail_handler.rb should be something like:

# Returns a Hash of issue custom field values extracted from keywords in the email body
def custom_field_values_from_keywords(customized)
  customized.custom_field_values.inject({}) do |h, v|
    if value = get_keyword(v.custom_field.name, :override => true)
      if v.custom_field.field_format == 'version'
        value = customized.project.shared_versions.named(value).first.try(:id).to_s
      end       
      h[v.custom_field.id.to_s] = value
    end
    h
  end
end

The problem is also in the current trunk.