Maintenance Planner not picking correct product instances installed

All,

I have built a new sandbox Enterprise Portal system and I am about to upgrade. Maintenance Planner is not picking up correct installed product instances. My old systems EP Dev, Qa and Prod systems have

Application Server Java

BI Java

Enterprise Portal

EP Core..

But the newly built SBX system is picking Application Server Java and BI Java automatically, and in Maintenance Plannner, under VERIFY it is giving 2 other installed instances to add Enterprise Portal and Developer Workplace. Why is this different for this system only? How do I correct? Is this correct and all other 3 systems wrong? How to add EP core? Please advise ASAP as I have to start upgrade ASAP, I had experience before if we did not choose proper installed instances in SMSY (usage type), some components will not be upgraded. I am afraid that might happen here as well. Please advise ASAP.

Below are installed components.

Also not sure about SAP CAF component question in below screen,

Other system have below usage types.

Thanks,

Kavitha Rajan.