The background transparent color setting has problems when using RMXP on more modern Windows versions. That's why it turns to a random pink/violet. Another effect of modern Windows is that the default save path for new projects no longer works, you have to relocate the project to "my documents" when creating it.
However, that transparency color problem is only a display problem in the editor - it doesn't affect the game.
If you have problems in your game, then this is something else and you need to give us a better error description...