The Characteristic Mode formulation for dielectrics solved with the surface equivalence principle (SEP) results in a set of eigen modes that contains both internal and external resonances. The internal modes (sometimes call non-physical or fictitious) do not radiate any power, and are thus removed from the result set. It is advised to increase the number of modes requested when dealing with such models.
From your description I understanding the the FEKO model was able to run through CADFEKO and that you then manually edited the PRE file through EDITFEKO.
In that case it is possible that you added a solution "card" in the PRE file above the FR card that defines the solution frequency. If such a card triggers a FEKO solution before the frequency is set, we would expect the error mentioned above.
As such, I would recommend that you check the order of the added cards to ensure that a solution is only requested after the FR card.