Tracking Token Problem

Hi all

I have a following problem:

I use tracking token with my emails in CRM(online). When I receive a replay message to email that has been sent from CRM, in most of cases the incoming email is associated with relevant record, according to the token. But, still there are few cases when incoming email wasn't associated with parent record of origin email.

Any suggestion what could be a reason?

The tracking token is a reliable for a 100%?

Thanks