When a visitor clicks on a affiliatelink on your website, the tracking duration starts. A transaction can only be allocated to your account if an affiliate link has been used. The tracking duration represents the time that a transaction, for a certain program, will be tracked.
Example
The tracking duration for a program is 30 days. This means that when a visitor clicks on a link on the 1st of june and does a transaction on the 29th of june the transaction will be allocated to your account. Except when that visitor has clicked on another publisher's link after your link.