First, I have to say, I’m not even certain it’s possible to have a link made when the user and the entry are not within the same site. So that very well could be the issue. I would need a super admin temp account and a regular user account so I could take a closer look. You can post the details here, just check the private reply box before submitting.
Now, it sounds like you setup Connections on your multisite to run in single site mode. Basically this mean Connections will use the same database across all subsites in which Connections is activated. I’m guessing this was done as part of the “previously raised with the multi-site usage” you mentioned??? What issue would that be? Could you give any info and background related to that?
One last question, on the subsite where you tried loggin in as a user, did you setup the role permissions on the subsite too? Setting it on the main site will not affect the subsite. That is by WordPress design in regards to roles and their capabilities.