petercasier on "SQL timeouts when bulk editing posts"

I run several WordPress sites on a Hostgator VPS. (PHP 5.3.20 and MySQL 5.0.96) and experience a weird problem:

All my sites run fast, all SQL operations are quite fast, MySQL and PHP variables are monitored and tuned with various tuning analyzers.

BUT, I experience long delays, often timing out, when I update certain meta-data in posts. E.g. when I "bulk edit" several posts, adding a new tag, the update is very slow.
Even updating one tag for one single post in the Posts > "bulk edit" menu, takes 45 seconds, on a server which does not seem to have resource limitations.

There are no errors logged in error_log...

Any hints in which direction I should focus my troubleshooting?