Re;
It work now. This is due to the PHP opcache extension. I've disabled it, restarted theimscp_panel and nginx services and this is now ok. I continue to investigate to know why opcache pose problem.
Edit
I've re-enabled opcache and this seem to work correctly now. In next release, I'll disable the fast shutdown opcache option. I'm pretty sure that this is the cause of the problem. If this problem occurs again, just disable opcache for the panel ( at bottom of the /var/www/fcgi/master/php5/php.ini file. and then, restart the imscp_panel and nginx services.
BTW: I don't know if opcache is really ready to use for PHP5.4. This could be also the problem...