This is rather annoying, maybe a bug/feature in Zend or something..
When using PDO_MYSQL, Piwik_Exec() calls ZendFramework which in turn uses the PDO driver's native exec() function. So, no profiling.
so this is a bug in Zend profiler
what was the reason to use Piwik_Exec instead of Piwik_query? does it bring better performance somehow?
Some queries (eg DDL) can't be prepared.
(In ) Fixes #2267 Each LOAD DATA INFILE will be profiled separately, but better than no profiling at all!