Based on your description, it sounds like you are experiencing issues with roller marks and uneven paint coverage on your basement ceiling after applying two coats of flat ceiling paint. Roller marks typically occur due to improper technique, the wrong type of roller cover being used or dry rolling. In this case, it could be that the paint was not applied evenly or that the roller cover left a textured finish on the ceiling. To address this problem, here are some steps you can take to fix it:

1. **Apply a Third Coat**: Consider applying a third coat of paint. Make sure to use a high-quality roller cover and apply the paint in even, overlapping strokes to achieve a consistent finish.

2. **Use a Paint Conditioner**: Adding a paint conditioner or extender to your paint can help improve its flow and leveling, making it easier to achieve a smooth finish. Follow the manufacturer’s instructions for the proper ratio to use.

3. **Check Lighting**: Sometimes, lighting can accentuate imperfections in the paint finish. Try viewing the ceiling under different lighting conditions to see if the issue persists. You may need to make adjustments based on how the paint looks in various lighting settings.

4. **Hire a Professional**: If the issue persists despite your efforts, consider hiring a professional painter to assess the situation and provide expert advice on how to correct the problem effectively.

Many ceiling paints are difficult to use. Requiring many coats ot even spraying to get then to look good. It is possible all that is needed is a better quality paint.