Actually, it may be very simple--what gears do you use when riding?
You should never have the chain in the extremes--IE in the large chainring and the large cog at the same time, or the small chainring and small cog.
Furthermore, the chain will be more likely to skip under increased load--IE if you try and climb in 7th in back and the big one in front
Also, the old chain could have stretched out--often times, a chain will actually stretch the teeth in the gears themselves. So, the new chain, even if sized properly, will still skip, until it can stretch out a little, and also stretch the gear teeth properly.
However, the new chain break in period should not take very long; if it does, it is something else.