I have dealt with this issue before.
When you ran
select count(1) UserTableColumnCount from information_schema.columns
where table_schema='mysql' and table_name='user';
you should have gotten 42. That's how many columns MySQL 5.5 has for
mysql.user. Since you got 39, that means you must have upgraded from MySQL 5.1. That has 39 columns.
I wrote an earlier post about the number of columns in
mysql.user in different versions : MySQL service stops after trying to grant privileges to a user
Here is the post where I dealt with this : mysql: Restore All privileges to admin user
Hopefully you could run
# mysql_upgrade --upgrade-system-tables
mysql.user and have it autofill missing permissions with
Give it a Try !!!
If you want to try to fix the mysql.user manually, here are the steps:
# Backup the mysql.user table
CREATE TABLE mysql.user_backup LIKE mysql.user;
INSERT INTO mysql.user_backup SELECT * FROM mysql.user;
# Add Missing Columns
ALTER TABLE mysql.user
ADD COLUMN Create_tablespace_priv enum('N','Y') NOT NULL DEFAULT 'N'
ALTER TABLE mysql.user ADD COLUMN plugin char(64);
ALTER TABLE mysql.user ADD COLUMN authentication_string text DEFAULT NULL;
# Give root user all privileges
UPDATE mysql.user SET
That's it !!!