I would like to suggest that whomever X/O the regulator didn't take the time to adjust the new one correctly. There are four rubber oblong covers on the bottom of the door. Two are for bolts that hold the bottom of the regulator. You can adjust the in/out angle of the glass. The other two are for tilt/up/down of the glass forward/aft. If it is too far out of adjustment, you can pull the panel off. There are two pinch clamps that hold the glass to the regulator. You need to get those right before the fine adjustments from the bottom. If your seals are not cracked, I imagine you just need to change both angles to block out the water.
I have replaced both of my regulators recently. It isn't all that hard, but a tad finicky to get right. The Bentley manual covers it completely.
Post a couple of pic's with the window/seal closed?
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