It's possible that it's a filter issue. The only way to test this would be to replace the filter in the IEM, if I'm not mistaken Etymotic does include an extra pair. You destroy the filter when you're taking it out BTW...
Have you tested to ensure you're getting a proper seal on both sides? A difference in seal can actually create a channel imbalance like this for some people. Test out foam tips on both sides (they'll always seal and about the same too) to ensure it's not the tips doing it (listen for imbalance, other changes are inevitable when changing tips).
The only other thing is that you may have your audio panned to the left or the right depending on what source you are using. Check your settings and ensure that this isn't the case. Many computers, and some mobile devices, allow you to change the L-R balance of sound (I know my Macbook and iPod does). Make sure that's centered as well. I only say this because I've had it go unbalanced for me on my Macbook and thought my jack was defective
Made me feel stupid when I figured out the issue.
If you've exhausted all of the above suggestions, contact Etymotic CS, they are generally really nice about warranty and IEM issues.