I also have used the companion cert with multi-city itineraries many times over the years. A couple of times the phone rep had to go check the rules, but they came back and said it was fine. You might just call reservations to see whether your itinerary is legit. They won't charge you just for telling you that.

Edited to add: Is your e-cert # in there when you try to hold? If so it may be that you can't hold the itinerary because of that. I've seen discount fares that couldn't be held before, so maybe this falls into that category.