When inline-editing a column in a row that has a column comment, the comment is included in the UPDATE query and breaks it, forcing a manual edit. For example, a "username" field with a comment of "The user's username" will result in a query similar to the following:
UPDATE somedb.users SET `name
The user's username` = 'Changed' WHERE users.id = 1
Cannot reproduce with a column containing a comment "The user's username".
Tested with phpMyAdmin 3.5.0-rc1
PHP 5.3.10
MySQL 5.6.4-m7
mysqli and mysqlnd
Firefox 10.0.2.
Please attach the export of your table's structure.