Fixed this for my installation by wrapping the column name 'category' in a trim function in the install_functions.php - eg:

$query = "SELECT project_id, trim(category) as category FROM $t_project_category_table ORDER BY project_id, category";
$t_category_result = db_query_bound( $query );

$query = "SELECT project_id, trim(category) as category FROM $t_bug_table ORDER BY project_id, category";
$t_bug_result = db_query_bound( $query );