So my soft top works great except for where the side windows meet the doors, the hard flaps keep coming open while im driving down the road. Anyone know the secret to fix this?

 

Are they tucked in all the way? (into the plastic surround then around the outside zippered)

 

You need to make sure that the front section is tucked in all the way. I usually start the zipper for just a few inches to secure it then tuck the front (where it meets the doors) in so only one stitch is showing. Once the front is all tucked in continue to zip all the way, finally tuck the plastic bottom flaps into the tub and secure the top and back Velcro.
Think that there is a video (from chrysler) somewhere on line that demonstrates this.