I have been redoing my boot again and i have found that these flaps(in the picture) cause a lot of sound. They are located near the antenna. If i put some foam in there to keep them open all the time will this cause any problems. Eg. condensation.

Does anybody have any idea?

condensation would occur anyway on a car in winter or any cold weather.
the vents are there to try and remove condensation while driving.

Would it make it any worse? Because it kinda creates a seal when it it closed but if i proped it open air can freely move between the boot and the outside..

The vents are there to suck air from inside the car while it is in motion. They are designed to shut when the car is stationary, sensibly to limit the amount of carbon monoxide ad other exhaust gases from entering the car. This works as the air vents will always force some fresh air into the car.

They work with positive/negative air pressure, positive air pressure comes in the vents, and pushes through the car, and when the car is in motion, it uses the air pressure over the car body to create an area of low pressure outside the car, hence the flap opens and air flows out.

Keeping these open all the time would be dangerous, you could get a large dose of carbon monoxide while in traffic, especially if you keep the ski-port open like I do. I have a feeling that modifying the action of these (always open) would be against ADR's, but I am not sure. Leaving them open all the time would actually lower SPL due to the fact it can 'leak' bass. If you wanted to do anything, i'd seal them shut, but again, could be breaking ADR's to do so.

That said, the vibrating plastic is alot quieter than say metal panels vibrating.

Thanks for your help. I think i might just leave them as they are.