I had a similar problem when I did my weatherstrips, this was before I knew about LEC so I sourced the strip from a different place and LEC had nothing to do with my problems.
I know just how jarred off you are, I ended up spacing out the holder I had manufactured, however this meant that the other edge didn't then contact the door skin, in other words the rubber was tight on the glass but then there was a gap between the top of the door skin and the start of the rubber.
The solution was to use masking tape along the door skin and apply black silicone sealent in the gap.

A word of warning however.....DO NOT BE TEMPTED TO USE LONGER SCREWS

, I managed to put 5 holes in the door skin before I noticed - moral of the story......
There is always someone worse off than you...and BRG IS a very very unforgiving colour!