[SalesForce] Why does an opportunity is not shown for the converted lead

I have an interesting issue where an opportunity that was closed of a converted lead, does not show on the relevant report.

1. A lead was created
2. The lead was converted to an Account + Contact
3. The account has only 1 contact
4. 2 opportunities were created – 1 was closed won, 2nd is still in process.
5. Under the contact's page – we only see the 2nd oppty
6. In the relevant report – I do not see the closed won oppty (I should [and I see] other opptys closed from converted leads)

I guess it has to do something with relating the oppty with the contact, but I don't understand why it's not happening by default?

Where do I fix this?

This breaks the money-flow and our marketing efforts.

EDIT: As per Techtrekker

I do see that the contact is registered as a contact role on one oppty (the open one), and not on the second oppty.

Adding the Contact to a contact role on the missing oppty: still did not add that data to the report (report of income from converted leads)

!!!!
Does this have an effect that we do NOT create an oppty on the lead conversion process? – We only create the oppty's AFTER the conversion is complete.

And if this is the case – how to solve it?

However, the role part is empty, and he is not marked as primary. In our org, we do not (never used) the contact role, isn't it by default that if a single user exists for a company, he becomes the primary ?