one of the problems was that the intro ep was shot and then the revised intro (War Zone) was made at the demand of TNT. Personally I thought War Zone was necessary, but that's just me.
but i digress. the problem arises from the original first ep which implies the Excalibur was loaned to Earth Force but Gideon was chosen by Sheridan to be the captain (w/ no explaination of why). I think there was a mention at the end of Call to Arms that the Excalibur was on loan for the duration of the search as well as the resources of the Rangers.
War Zone was purposely written to exclude and refs to B5 or Sherian (even the Alliance) so the Excalibur become an Earth Force ship (Dureena is arrested when Sheridan should have vouched for her, Sheridan choosing Gideon isn't mentioned, etc).
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"I bring the hand of God and that's all I bring. I speak for the Hand of God. I am the Preacher"
The Preacher - Dune Messiah