Oh dear. that doesn't sound good at all Kay.
Sitting her in ours, looking at our front window/winder & trying to imagine where the water could be coming from... considering you now have the new cover outside. I would imagine the top sail track would prevent water getting to the window frame... assuming it has been stuck on properly.
Stuck on, or stuck & screwed on?
Thinking back to our Winnie. Had a sail track added above the rear window for a shade cloth attachment... it was Sikaflexed & screwed... but... the RH side screw hole had not been sealed/Sikaflex prior to inserting the screw - self tapper. Consequently water eventually dribbled into the cavity between the window & the corner of the Winnie causing minnie sideways stallegmites to form on the inside of the inner panel.
Damaged panel was cut out & replaced - under 'warranty' - courtesy of a friend in the right place at the right time.
Winnie was 4 years old at the time.
Hope your problem is easier to find & rectify.