Mixcraft's metronome has a count-in feature you can turn on, but if everything sounds good before you mix down, there's something else going on. The mixed-down audio should sound the same as the audio when you play the project.
First, what version and build of Mixcraft are you using? Choose "Check For Update" from Mixcraft's help menu to make sure you've got the latest.
If that doesn't fix the problem, try mixing down to a wav file that has the same sample rate as your project. If you are using WaveRT, this will often be a sample rate of 48000 Hz. Why would this help? Some plugins can't handle sample rate changes upon mix-down.