Please take note of the garbage collection "feature" on systems like Ubuntu and Debian.
apt-get installs a cron script at /etc/cron.d/php5 that checks the session.gc_maxlifetime variable and then deletes all old sessions every 9 and 39 minutes.
The problem is: If you set the maxlifetime for a specific virtual host, those settings will be ignored. Lets say you want your server to store sessions for only 30 minutes, but for one special website you want all sessions to be 24 hours. If you set the session.gc_maxlifetime in .htaccess, your apache conf or use ini_set in your code, it won't work and sessions will still be destroyed after 30 minutes. That's because /usr/lib/php5/maxlifetime (found in that cron file) will always return the value in your php.ini, not the values you set in .htaccess.
A workaround is to set the maxlifetime to the maximum your sites require, and then configure a shorter maxlifetime in your .htaccess for those sites that don't need it.
Another solution is to give the php5 file in /etc/cron.d sane values, ie, only let it run at 3am in the morning, but you'll have to remember to block the replacement of this file it every time you update php.