I found it takes a little bit of fiddling to get the trunk seal in proper position under the metal lip. Push it into the upper corner under the lip with your finger tips, then into the lower corner. When it goes in right, you'll know it. Once it's all in, it's a good idea to lubricate the contact surface with silicone. If the lid/seal contact can't slide a bit, it can bunch up the seal and distort the lid at front center.
George Davis
'69 280 SL Euro manual