As above, email notifications of new posts in subscribed threads don't contain a link to the post, just the main site link.
Has alternative forum software been considered, such as http://www.simplemachines.org
/? There seem to be a lot of issues with the current software, and I've been running two SMF forums for a number of years without any such problems.
Remember to deliver with the speed of light
A little bit of love and joy