Angie, one of the things that you should be looking at is ice damming. With cold, snowy winters like we have had this year, ice buildup at the edge of the roof can allow water to back up under the shingles and find an entrance into the interior framing. Once the water is inside, it allows the growth of molds.
It is impossible for us to tell exactly what is happening with your house from your brief description so you should check with a local pro.
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