Hello ;
You have done the upgrade in wrong way... and on next i-MSCP upgrade, you'll have some problems because the i-MSCP installer doesn't know much about the MySQL server version 5.5 which is provided by the dotdeb repository. Normally, to switch to another SQL server, you must rerun the imscp-autoinstall script as follow imscp-autoinstall -dr sql but it's now too late...
Well, for now, you can fix your problem as follow:
Edit the /etc/imscp/imscp.conf file and at bottom, change the SQL_SERVER parameter value to mysql_5.5 manually. Once done, rerun the imscp-setup script and normally, your PhpMyAdmin version will get updated.
Note: On the next iMSCP upgrade (when you'll run the imscp-autoinstall script), you'll have some problems (see above)). Thus, you'll have to edit the squeeze packages file to add the MySQL server version 5.5 as provided by the dotdeb repository. I bet you 'll ask me in time for that 
Update to new PMA worked, thanks.
You're talking about apt pinning in ./docs/Debian/packages-squeeze.xml, aren't you? That won't be a problem
Re;
I don't talk only about the pinning You'll have to add a new section for mysql_5.5 with your own repository (dotdeb) to make the installer aware of this alternative Look at the packages files to understand how you can add your own sections using your own repositories.