It is possible that Intel legal knew that NVIDIA was complaining that Intel was using its Interpretation of the License Sharing Agreement and Intel's IP to prevent NVIDIA from entering the chipset market for Intel processors.
Intel legal may have felt that after negotiations broke down, the best thing they could do was seek Declaratory relief to get a Court's opinion on the correctness of their position.
This action is still pending. The FTC may have felt that they would lose a jurisdictional turf war if they allowed an Article I court to resolve the problem. So they rushed a complaint in a race to (jurisdictional) justice.
It would not surprise me, assuming no relevant statutory directive to see Intel file an injunction requesting a Federal Court to order the FTC to stay its proceedings until the matter could be heard in Court. ... on the other hand, Intel might risk that the Court will stay it own proceedings until all administrative procedures have been exhausted.
As Bono once quoted, "Drums keep pounding a rhythm to the brain, La de da de de, La de da de da....."