Modern materials strike again. This problem never occured with the old reinforced tar felt. Basically who ever fitted the membrane did not stretch it over the roof rafters, so it is now flapping about in the wind. Not any easy fix unfortunately. I think you have three choices.
1) Increase the depth of insulation above the ceiling using rock wool.
2) Cut 25mm insulation board and stick it in between the rafters against the felt.
3) Spray or paint the areas that are flapping about, with some sort of glue, this may make the felt more rigid and stop the flapping. However this requires caution as some glues contain solvents that might melt the felt. If you do decide to use a glue , try a small area first and make sure it does not damage the felt. Also read the Health and safety warnings on the spray cans, some of that stuff is really bad if you breath it in.
Hope this helps, let us all know how you get on.