Please don't double post. New postings have to be moderated before they go live.
You need to describe what you're recording, how everything is connected what computer you have, operating system and which version of Audacity.
When you're recording, do both red recording meters move exactly the same. They may not be at the same level, but they never break lock step?
Meters are going to be important here, so you may want to make them bigger. Grab the right edge of the meters and pull sideways.http://kozco.com/tech/audacity/Audacity1_record.jpg