Ops identified the same problem down here.
Here is the thing: on some FMS, if you edited somehow the route to the alternate, you would have no alternate predictions at all. It was a software bug which was fixed later.
It was called something like "Erroneous Alternate Fuel Predictions Upon Modification of a Company Route"
Whenever we found the same situation, we would erase the alternate, add it again, and did touch the route to it (i.e. adding a star to the route).
Hope that helps!