even if i dont do any changes, as soon as i check off the use default rule in the earth scenario, my science tree in the game gets screwed up and i cant choose which ones to research.........

does this thing happen to anyone else?

It seems if you make any of a long list of certain changes it screws up the game when you choose Load Scenario. Try just replacing your main civ3mod.bic (back it up first) and choosing "New Game" instead. All your changes are automatically present, and should work just fine.

So really, making an actual "Scenario" is pretty much impossible. Doh!