Ok we have been banging our heads against the wall for weeks on this. We are using Salesforce and Marketing Cloud with the Salesforce connector.
Our workflow looks like this
TRIGGERED SENDS
We have several triggered send emails that have been setup in Salesforce. We set up the rules in salesforce and link them to an email in Marketing Cloud. These are sent usually whenever someone opts in. We also have daily emails that go out using Automation Studio and a query. I am not sure, but I don't believe these are set up in Salesforce. I'm pretty sure they were all set up directly in SFMC.
MANUAL SENDS
We send several manual sends. These are created in SFMC and sent entirely from SFMC.
MANUAL SENDS SHOW UP IN REPORTS, TRIGGERED SENDS DO NOT
They both seem to be tracking in Salesforce. I see individual email results on both and aggregate link level results on both. But TRIGGERED SENDS aren't showing up in reports that are built, while MANUAL SENDS do.
We discovered that the difference between the two types of sends is that Triggered Sends are missing a send definition. 
We know this is the issue because when we manually add a send definition to an individual triggered send email result, it shows up in reports.
The problem is that I don't know why triggered sends are not getting a send definition. There are triggered send definitions in SFMC and they are running and appear fine. But for the life of me, I cannot figure out why the individual email results don't have the SendDef in Salesforce…??? Thanks in advance for any help you can give.
Best Answer
Triggered Sends do not use the same Send Definitions as User Initiated sends and the likes, they use Triggered Send Definitions. The Individual Email Result object created in your CRM Org has an attribute called "et4ae5__TriggeredSendDefinition__c". Use this for grouping in your report.