MySQL 5.5 : "Got an error reading communication packets" - mysql

Question

I just upgraded MySQL from 5.1 to 5.5.
I fixed few issues running mysql_upgrade, and changing some deprecated configurations...
I also updated PHP, from 5.3.3-7 to 5.3.29-1.
But, since that, I'm having a reccurent problem (always thrown in this order) :
1. Client* - PHP Warning
Warning: Packets out of order. Expected 1 received 0. Packet size=1 in
/home/www/www.mywebsite.com/shared/vendor/doctrine/dbal/lib/Doctrine/DBAL/Connection.php
line 694
2. Client* - PHP Warning
Warning: PDOStatement::execute() [pdostatement.execute]: Error reading
result set's header in
/home/www/www.mywebsite.com/shared/vendor/doctrine/dbal/lib/Doctrine/DBAL/Connection.php
line 694
3. Server* - MySQL Warning :
150127 17:25:15 [Warning] Aborted connection 309 to db:
'my_database' user: 'root' host: '127.0.0.1' (Got an error
reading communication packets)
4. Client* - PHP Error
PDOStatement::execute() [pdostatement.execute]: MySQL server
has gone away in
/home/www/www.mywebsite.com/shared/vendor/doctrine/dbal/lib/Doctrine/DBAL/Connection.php
line 694
*NB: What I call "Client" is the PHP Application, and "Server" is the MySQL Server, even if they're both on the same localhost Server.
So, apparently, the origin of all those problems is the first one : "Packets out of order".
But when I search for this error I can't find many answers, and they are most of the time not related to my problem : I use Doctrine as an abstraction, so I don't write any query or fetch any result myself. Plus, it's almost never the same values as me, but in my case I always get those values ("Expected 1 received 0. Packet size=1").
The closest result would be this MySQL bug report, but "No feedback was provided for this bug for over a month, so it is
being suspended automatically"...
Plus, some of the "2." errors aren't thrown by my PHP Doctrine code (they're not executed from my localhost, but from another known external service, probably using some old PHP Propel code).
So that might mean there is a problem with my MySQL configuration itself, but I tried changing some parameters without obtaining any obvious effect (sometimes it takes more time after restarting MySQL to get the first errors for example).
Any help would be very much appreciated !
And here is my current configuration (I've got 2 MySQL instances, the second one using replication is mostly for read only).
I also checked most of the system resources with Munin and didn't see anything abnormal (the RAM usage for example is pretty high, but as there is 50Go on the server it's not full at all).
UPDATE
I isolated an SQL query that was repeatedly failing from my PHP Client. When I executed from my local with MySQL Workbench, it did exactly the same (closed the connexion with a MySQL server has gone away message). When I did it from the sql command line it also did the same. Then I executed it from the sql command line on the server host, and it succeded. But some time after when I tried again from Workbench/whatever it worked... So it looks like those "corrupted packets" are cached and disapear after some time.

Answer 1

Thanks, I fixed this issue doing :
RESET QUERY CACHE;
FLUSH QUERY CACHE;