[Paul F]

It sounds like you have the answer. Misfit valve covers.

1. Pictures - show us what you mean about the gaskets sticking out
2. What valve covers are you using
3. What type of gasket material are you using
4. Are you using silicon on the gaskets
5. Are the valve cover seats distorted? Don't torque them down so hard that you now have high spots in between the bolts

This should not be a problem. It's likely some issue with the covers.