The door seal DOES NOT block the drain holes in the bottom of the doors.
I'm probably wrong, I just got that impression...
Now we are getting some where, your doors have been reskinned? I had this on the door I had reskinned, the weather strip would not contact the window at one end, i ended up fettling the panel where the weather strip is fitted to get it to sit some where right.
Yes the doors have been reskinned. As I say it IS in contact all the way along...it's just the seal is further away in the middle than at the ends (less pressure against the glass in the middle). This is the only thing I can see which would affect how well they would work, but as I say there is contact all the way along so it seems odd.
Also check that if the bottom of the door has been repaired, which is usualy the reason for the new skin, that all the drain holes are still present
How many holes should there be??