"This reservation is not eligible to be upgraded"
 

My parents just booked a LAX-SFO-ZRH and CDG-LAX via their cruise line. It's one PNR with the LAX-SFO leg booking into B, and the SFO-ZRH leg booking into R. The return is on AF booking into A. When I click the "Upgrade Cabin" link, I get the error message that "This reservation is not eligible to be upgraded". Is it because of the AF leg? When I click on "Fare Rules", I just get an endless spinner.

Most likely the reservation hasn't been ticketed by the cruise line. If they booked a "flexible" fare through the cruise line, it won't be ticketed until after final payment or 30 days before departure. Once it is ticketed, the ability to upgrade may appear.

Note: This has nothing to do with paying the cost of the airfare to the cruise line. You may have paid for the airfare to the cruise line, but the cruise line has contractual agreements to delay payment until as close as 30 days from departure. This has the advantage to the passenger of often being able to change and/or cancel the flight without penalty while locking in the price of the airfare.

Probably the travel agent has not yet ticked the flight. Travel agent or cruze line. Unless it is some special combo cruze fare booked in basic.

Yep, another vote for it just not being ticketed yet. Same thing just happened to me when booking through an OTA.