Closing the lid isn't going to hurt anything. In fact, closing the lid help's keep air born contaminants from getting in. What ever the smell is it's likely that it was already there, and closing the lid just locked the smell in.
1. What does it smell like? Is it a musty smell or smell like mold?
2. What is the water temperature?
3. What
nutrients are you using? Do you have a link to them online?
4. How does the water look? (is it translucent or cloudy)
5. What are you using for the water source?
6. Is there any foam on top of the water?
7. Along with the nutrients, are you using any additives?
8. How do the roots look, are they white and strong, or brown/black and slimy.