Well I've had the same kind of problems with individual VCs, and I never solved them satisfactorily.
Even when you set global victory to personalize, and there tick off every option, it seems that "conquest" remains as the default VC. But I have played one scenario where conquest was disabled for good. Dunno how it is done...
What I have resigned myself to is add another civilisation with a tower hidden in a corner of the map where the player will never find it. It effectively disables "conquest" even if it's not very elegant...
As for the fact that your VCs don't work, it's not linked with "conquest" : remember that victory is achieved when EVERY player in a team has completed their individual VC, or when then team has completed the global VC.
So I can only two causes for your problem :
1) Your player has an ally with different VCs. In that case, just to be sure, a) set to the ally an individual VC that it cannot fail to meet b) check diplomacy and "victory as a team".
2) A bug. Individual VCs are thoroughly bugged. Even worse, they sometimes work, sometimes don't, with the same scenario. Or depending on when they are achieved : they will work at the start of the game, but will be ignored after some time into the game... Especially concerned is the destroy a # of units VC : avoid it at all cost !
In my scenario "evasion" for instance, "bring object to area" didn't work, at least not reliably. I had to use "bring object to object". In "Legions from Hell" I just discovered that the VC for the CP opponent did not always worked : I'd had no pb with that scenario, but last week a friend of mine played it, and when the CP met its VC (build one wonder) the game did not end. That scenario had been extensively play-tested, and still...
So, as a conclusion, although individual VCs are a great fixture (and, hey, ES : we also need individual GAME LOST conditions !!, try tweaking global conditions to suit your needs as much as you can.
To illustrate this, let's take my "Legions from Hell" scenario : I didn't standard VC because there's an artifact and a ruin also. The CP starts the game with an artifact, and there's no way the player can get at it before the 2000 years mark. In the same way, the player is not supposed to win by just discovering the ruins. But there was a way around it : a portion of the map is off-limit to the player and the various CP... Putting there a gaia ruins and a gaia artifact would have enabled me to use standard VC. And the scenario wouldn't be bugged !