I've had this same problem, I installed a mod and when i used the mod launcher, it brought me into origin and the regular zero hour.
Mods don't work with the Ultimate Collection, but you can use these fixed installers: http://www.commandandconquer.com/forums/showthread.php?8350-Fixed-Launchers-for-The-Ultimate-Collect...
I experienced the same result...d/l and installed launchers to Origin Directory and game launched to Origin to select Generals/Zero Hour just as it did before.
i also cant seem to get any mod to run. Not to mention, even the root EXE for the game, brings you into Origin which Origin launches the actual game. **bleep**ed up EA, thats **bleep**ed up!
Every Mod Users!!! Got a fix! http://bibber.bplaced.net/downloads/cnc-3-kanes-wrath/the-ultimate-collection-fixed-launchers/
Download it and then install it and it will work