instruments distort each other

[picato]

Sometimes you can get problems like this, and the first thing to check is, just like the boys already suggested, clipping...
But it isn't necessary a phenomenon about clipping. A snare and a basedrum can easily create some strange effects together. You could also use a spectralizer to make sure that the peaks of the sounds doesn't occupie the same frequencies. If that's the case, a notch filter on that frequencies can fix the problem. An other way to go is trying to move one of the sounds one or two milliseconds back or forth in the song. This way the peaks doesn't occur at the samt time, but you want notice the very slight latency either.

When mixing a real bas guitar and real drums you can get a really different sound by experimenting whith slight latency. I have not tried this one on synth music though, so I dont know if it works on this type of sounds. Mixing electronica and ordinary pop/rock isn't the same thing at all...