This is the second time I read your topic post question. I guess I was hoping someone else could answer with confidence. However, I can tell you how it should be working.
After your save to cpx/cpn.
The 'first' scenario in the list of scx/scn's that are saved into cpx/cpn should appear in the sub-list when opened in the Single Player, Custom Campaign. (only this first one should appear).
If player one wins the 'first' scenario, then the 'second' scenario should also appear in the 'Campaign' sub-list. (appearing under the first on the list).
This list should grow with each player one victory.
The list should remain in the order that it was saved.
Each scenario that has been completed to victory will then be in the list, and available for replay.
I'm sorry that I cannot help you to answer why your saved Campaign is not doing this.
My suggestion would be to set up the scenarios for saving under a *new name*
Save and open in Custom Campaign for play.
If you see the first scenario in the sub-list, select to play it. Once the game begins, open your chat interface and enter the IRWINNER cheat code. Do this for all scenarios in your campaign to test if they are working and in the right order.
Install patches: I'm not sure, but I think the patches did have some editor related fixes.
The last suggestion I have is to open windows explorer, and pull to another folder all your custom campaigns, scenarios, AI's, saved games, sounds, etc. (Saving these created custom files), and then reinstall the game.
I'm sorry I could not be more helpful and realize I may have just outlined many things you have already tried. What you are describing should not be happening, and is a bug of sorts.
"I take it that this is the Anastasia Scud pines for?" - Epic Commander
"What Ana said. Use sugar and the whip." - aka the Pilot
"I think you will realize the emphasis was on Ana and Cake." - Monk