I am currently having problems with a 3 user install where the Magnet works fine for 1 user but not for two others. I have had situations where, although mail does not show in the Magnet it does appear in the email related items for the contact and also instances where it does not appear under the contact - which is really bad news.
In both cases where the Magnet fails and the emal does not appear under the contact, I know the email has been matched because if I click the CRM link at the bottom of the email, it will allow me to create a task which then appear on the contact.