This problem has been tackled before......It's a common fault.
If the glass is the wrong shape it cannot physically 'push' the rubber out to the aperature(where it's supposed to be)
A lot of the aftermarket glass is poorly shaped too,result...water leaks.
To be told it's not a problem is
wrong!Judging by the fact it leaks seems to confirm this......
As IsolationRide said, if it's a show truck re-do them.
If you don't want to go down that road,your only option is to try and seal them in situ.
There are many sealants available,try contacting another 'reputable' glass shop. They would be able to suggest something suitable.Personally I would use a urethane based sealant.That's my preference.
As long as it's not silicone!
