Quote; Silicone sealant will fill gaps well.
I tried this once and OK it worked, but some time later I had a pane of glass broken and it was a devil of a job to repair. The stuff stuck like the proverbial to a blanket.
Back to the question; The rubber seals may have perished and blocking the water channels below.
I found removing the seals altogether and sitting the glass directly on to the aluminium works OK and the channels remain clear.
The choice is yours.